How to Run Payroll in South Sudan: Employment Taxes & Setup

Milani Notshe

Research Specialist

Last Updated

February 13, 2026

In This Guide

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Running payroll in South Sudan involves many moving parts before your team sees money land in their accounts. Each month you need to calculate gross-to-net correctly, apply statutory withholdings and employer contributions, issue compliant payslips, plus file and remit on schedule. If anything slips through the cracks, you could face penalties, back-pay exposure, and unnecessary friction with your people.

If you’re hiring in South Sudan, whether you’re building a local presence or expanding your global footprint, this guide is for you. We’ll walk through the choices and compliance requirements that have the biggest impact on your speed and risk, from entity vs. no-entity hiring to worker classification and the statutory bodies you’ll interact with along the way. By the end, you’ll know exactly what to expect and how to keep payroll running smoothly, wherever you’re hiring.

Key Takeaways

Payroll cycle: Employers in South Sudan generally process payroll on a monthly basis.

Tax filing: Income tax withholdings and relevant statutory deductions are typically reported and remitted monthly, though procedures may vary depending on local administration.

Employer taxes: Employer obligations may include social security and other statutory contributions where applicable, with requirements differing by sector and evolving regulations.

Tax year: South Sudan follows the calendar year for tax purposes, from January 1 to December 31.

Payroll processing methods: Payroll is commonly handled in-house or outsourced to providers familiar with South Sudan’s developing tax and compliance framework.

How to Choose Your Payroll Structure in South Sudan

Expanding into South Sudan? Building a compliant payroll setup involves much more than simply paying salaries. You’ll be responsible for employment compliance, monthly tax and social declarations, and mandatory benefits. Even small delays in filings or payments can lead to real penalties.

You have several operating models to choose from to make this easier. The right one depends on your legal footprint, your appetite for risk, and how quickly you need to start hiring. Let’s break down the main options and when to use each.

1. No Local Entity in South Sudan: Use an Employer of Record (EOR)

If you don’t yet have a legal entity in South Sudan, an Employer of Record is usually the fastest and lowest-risk way to hire. An EOR becomes the legal employer on paper, provides locally compliant employment contracts, and manages payroll under local regulations, while you continue to direct the work and manage performance.

This model is ideal for:

Testing a new market
Hiring your first team members
Scaling a distributed workforce without building local infrastructure,

Why it’s the fastest and least risky option:

You skip the lengthy process (and cost) of setting up an entity.
All local registrations, monthly declarations, and statutory payments are handled by a provider already set up in-country, dramatically reducing your compliance risk.

2. You Have a South Sudan Entity: Run In-Country Payroll

If you already operate a local entity, or you’re planning to establish one, running payroll directly gives you maximum flexibility and control. You can set your own policies, design benefits, and align payroll closely with your finance and internal approval processes. But this also comes with greater operational responsibility.

What you’re responsible for:

Registering with relevant authorities and maintaining compliance with statutory bodies (often involving CSS/IPRES or similar local institutions).
Accurately calculating and remitting payroll taxes and contributions every month – plus handling year-end requirements.
Issuing compliant payslips and maintaining audit-ready payroll documentation.

When this option makes sense:

You’re hiring at scale and want payroll fully “in-house,” even if you partner with a local provider for execution.
You need deeper integration with finance systems or custom benefit structures.

If you want to keep the entity but offload the admin, many employers choose global payroll services to handle calculations, filings, and payments while they remain the legal employer.

3. Contractors Only: Use Contractor Management

Paying independent contractors is often simpler than setting up full payroll, especially for short-term or highly specialized work.

However, you need to watch out for misclassification risk. In South Sudan, as in many jurisdictions, someone may legally qualify as an employee based on how they work – not what their contract says. If they’re under your direction, working like an employee, you may be responsible for full employer obligations.

When contractor payments work well:

You need specialised expertise for a defined scope or timeframe
The contractor operates independently, not under your control or supervision

You can also use contractor management services to streamline compliant contracts, invoicing, and payments.

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What To Know About Payroll Processing In South Sudan

Payroll in South Sudan centers on correctly withholding personal income tax, calculating any statutory contributions, and remitting these amounts to the National Revenue Authority (NRA) within the required timelines. You also need to manage employer obligations such as registration, monthly payroll reporting, and maintaining detailed records that can be inspected during tax audits. Requirements can differ depending on employee income levels, contract type, and whether you operate through a local entity or via an Employer of Record.

Non-compliance can trigger penalties, interest on late payments, and potential suspension of your tax clearance, which can disrupt work permits, tenders, and banking relationships. Errors in payroll can also damage employee trust if net pay is inconsistent or if tax certificates are missing or incorrect. This guide walks you through how to structure payroll calculations, understand the main tax types, meet filing and payment deadlines, and set up compliant processes for your team in South Sudan.

Types Of Payroll Taxes In South Sudan

In South Sudan, payroll taxes are primarily governed by the Personal Income Tax Act and administered by the National Revenue Authority, with employers responsible for withholding and remitting tax on employment income. Your main focus will be on Pay-As-You-Earn (PAYE) income tax, any applicable training or skills levies, and withholding on certain allowances or benefits that are treated as taxable income.

Pay-As-You-Earn (PAYE) Personal Income Tax

PAYE is the core payroll tax in South Sudan and is withheld from employees’ taxable employment income each month. The system is progressive, with typical brackets ranging from 0% on very low income up to around 15%–20% on higher earnings, calculated on cash salary plus taxable benefits.

Employers withhold PAYE from each payroll run and remit it to the NRA, usually on a monthly basis shortly after the end of the pay period. Late or underpaid PAYE can attract penalties calculated as a percentage of the unpaid tax plus interest, and repeated non-compliance can trigger audits and restrictions on your tax clearance status.

Withholding On Allowances And Benefits

Certain allowances and in-kind benefits provided to employees, such as housing, transport, or hardship allowances, are treated as taxable income and must be included in the PAYE calculation. In practice, this means that the same progressive PAYE rates of roughly 0%–20% apply to the total taxable package, not just base salary.

Employers must maintain clear documentation of each allowance, its value, and how it was taxed, and they must reflect these amounts on payslips and annual tax certificates. If allowances are misclassified as non-taxable, the NRA can re-assess the employer for the unpaid tax plus penalties, and may also hold the employer liable even if the employee has already left the company.

Training Or Skills Development Levy

Some sectors and larger employers may be subject to a training or skills development levy, typically calculated as a small percentage, often in the low single digits, of the payroll cost. Where applicable, this levy is paid by the employer on top of gross salaries and is not deducted from employees’ pay.

The levy is usually reported and paid on a monthly or quarterly basis together with other payroll-related filings, using the same employer tax identification number. Failure to pay on time can result in surcharges and may affect your eligibility for government contracts or sector-specific licenses, so your payroll calendar should track these obligations alongside PAYE.

How To Pay Employees In South Sudan

Most employers in South Sudan pay employees via bank transfer in South Sudanese pounds (SSP), although cash payments are still used in remote areas where banking infrastructure is limited. You should align your pay cycle with local practice, which is typically monthly, and ensure that salary is paid on or before the agreed payday stated in the employment contract.

If you do not have a local entity, you can use an Employer of Record to hire and pay staff compliantly, or work with a local payroll partner while you complete entity registration. Payslips should clearly show gross salary, each taxable allowance, PAYE withheld, any other deductions, and the final net pay, and they should be provided in a durable format that employees can keep for visa, loan, or tax purposes.

Payment Method: Use bank transfers in SSP where possible, resorting to cash only when employees lack access to banking services.
Pay Frequency: Set a consistent monthly pay date and document it in employment contracts and internal policies.
Currency Management: Convert foreign funding into SSP in time to meet payroll, accounting for potential FX and banking delays.
No-Entity Hiring: Engage an Employer of Record if you need to hire quickly without establishing a South Sudanese legal entity.
Payslip Content: Include gross pay, itemized allowances, PAYE, other deductions, and net pay on every payslip.
Record Keeping: Store payroll records and payslips securely for several years to support audits and employee requests.
Bank Compliance: Ensure your company bank account is KYC-compliant and authorized for salary and tax payments.

Payroll Set Up Checklist (Entity Vs No-Entity)

Getting payroll set up correctly in South Sudan is essential because your tax registrations, bank arrangements, and employment contracts all feed into accurate monthly calculations. The process differs significantly depending on whether you operate through your own local entity or rely on an Employer of Record to handle compliance on your behalf.

With a local entity, you are directly responsible for registering with the National Revenue Authority, configuring payroll software, and filing returns, while a no-entity model shifts these obligations to your EOR partner. In both cases, you should design clear approval workflows, data collection processes, and audit trails before you run your first payroll.

Incorporation Or EOR Choice: Decide whether to register a South Sudanese entity or use an Employer of Record for hiring and payroll.
Tax Registration: Obtain an employer tax identification number with the National Revenue Authority before hiring staff.
Bank Account Setup: Open a local SSP-denominated bank account capable of processing salary and tax payments.
Employment Contracts: Draft written contracts that specify salary, allowances, pay frequency, and termination terms.
Payroll Data Collection: Collect employee IDs, bank details, tax information, and signed contracts before onboarding.
Payroll System Configuration: Configure payroll software or spreadsheets with local tax brackets, allowances, and reporting formats.
Internal Controls: Establish maker-checker approval for payroll runs and tax payments to reduce errors and fraud.
Reporting Calendar: Build a payroll calendar that tracks all monthly and annual filing and payment deadlines.
Document Retention: Implement a policy for storing payroll records and tax filings for the legally required period.

Example Of Salary Tax Calculation

Imagine an employee in Juba with a monthly gross salary of SSP 300,000, including base pay and taxable allowances. You would first determine the taxable income, apply the progressive PAYE brackets, and then calculate the PAYE amount to withhold for that month.

Once PAYE is calculated, you subtract it from gross salary to arrive at net pay, which is then transferred to the employee’s bank account. You must also record the PAYE withheld in your payroll ledger and prepare it for remittance to the NRA within the required deadline.

Step 1 – Confirm Gross Pay: Add base salary and all taxable allowances to reach the total monthly gross of SSP 300,000.
Step 2 – Apply Tax Brackets: Split the SSP 300,000 across the applicable PAYE brackets and apply the corresponding percentage rates.
Step 3 – Sum PAYE: Add the tax amounts from each bracket to determine the total PAYE to withhold for the month.
Step 4 – Calculate Net Pay: Subtract PAYE and any other authorized deductions from gross salary to get net pay.
Step 5 – Record And Remit: Record the PAYE liability in your accounts and schedule payment to the NRA before the due date.

Submitting Employee Tax In South Sudan

Employers submit PAYE and any related payroll taxes to the National Revenue Authority, typically using prescribed forms and payment instructions issued by the local tax office. You will need your employer tax identification number, a breakdown of total taxable payroll for the period, the PAYE withheld, and supporting schedules for each employee.

Tax Office Registration: Ensure your business is registered with the relevant NRA office and that you know your filing location.
Manual Or Portal Filing: Use any available NRA e-filing portal or submit physical returns where electronic systems are not yet in place.
Bank Payment: Pay PAYE via bank transfer or deposit using the reference details provided by the NRA.
Payroll Software Exports: Generate employee-level PAYE schedules from your payroll system to attach to your return.
Third-Party Support: Consider using a local accountant or payroll provider to handle submissions if your internal team is new to South Sudan.

Payroll Tax Due Dates In South Sudan

Tax Type	Due Dates
Monthly PAYE Withholding	Generally due by the 15th day of the month following the month in which salaries are paid.
Training Or Skills Levy (where applicable)	Typically due monthly by the 15th of the following month, aligned with PAYE submissions.
Annual Employer PAYE Reconciliation	Commonly due within three months after the end of the financial year.
Annual Employee Tax Certificates	Usually to be issued to employees within three months after the financial year-end.
Amended PAYE Returns	Should be filed as soon as an error is identified and before the next routine payroll audit.

Running Payroll Processing in South Sudan

So, what does it actually take to run payroll in South Sudan? It involves calculating monthly salaries, applying the right statutory deductions, and making sure your team gets paid accurately and on time, while staying fully compliant with local tax and labour laws.

Let’s walk through what that looks like in practice:

Monthly Payroll Workflow

Gather all the essentials: hours worked, leave taken, new joiners, leavers, and any salary or benefit changes.
Double-check timesheets, leave balances, overtime, and any variable pay to make sure everything is accurate.
Work out gross earnings, including base salary, bonuses, commissions, and allowances.
Apply mandatory and voluntary deductions, like income tax, pension contributions, benefits, and any company-specific deductions. Then, calculate net pay after all deductions.
Run internal reviews, compare with previous payroll cycles, and get the necessary approvals.
Pay employees via bank transfer and share payslips through email or your payroll system.
Send statutory payments and required reports to tax authorities.
Update your records and ensure payroll entries flow correctly into your accounting system.
Share payroll summaries with finance and address any open questions or discrepancies.

How Playroll Streamlines Processing

Keeping track of all these steps, especially in a new market, is no easy task. Regulations change, requirements shift, and it’s easy for things to fall through the cracks. Playroll makes this effortless by managing the entire payroll process for you: onboarding employees, handling calculations and deductions, issuing payslips, transferring funds in South Sudanese Pound, and taking care of statutory filings and compliance.

Income Tax And Social Security In South Sudan

Understanding the tax obligations for both employers and employees is crucial when operating in South Sudan's business landscape. This section explains how taxes and statutory fees affect payroll and individual earnings in South Sudan.

Employer Tax Contributions

Employer payroll contributions are generally estimated at an additional 2% - 5% on top of the employee salary in South Sudan. This range reflects potential training or skills levies and other sector-specific charges that may apply to larger employers or regulated industries.

Tax Type	Tax Rate
Employer Training Or Skills Levy (where applicable)	2% of total payroll
Occupational Health And Safety Or Inspection Fees (sector-specific)	Approximately 1% of payroll in applicable sectors
Work Injury Or Insurance Premiums (private schemes)	1%–2% of payroll depending on risk profile
Administrative Payroll Compliance Costs	Approximately 0.5%–1% of payroll in internal or outsourced fees

Employee Payroll Tax Contributions

In South Sudan, the typical estimation for employee payroll contributions cost is around 10%–20%.

Tax Type	Tax Rate
PAYE On Low-Income Bracket	0%–5% of monthly taxable income
PAYE On Middle-Income Bracket	10% of monthly taxable income within the band
PAYE On Higher-Income Bracket	15%–20% of monthly taxable income within the band
Tax On Taxable Allowances	Taxed at the same progressive PAYE rates as base salary
Withholding On Bonuses	Included in taxable income and subject to standard PAYE rates

Individual Income Tax Contributions

Individual income tax in South Sudan is charged on a progressive basis, with higher earners paying a higher percentage of their taxable income. Employers act as withholding agents, but individuals with multiple income sources may need to reconcile their tax position directly with the NRA.

Income Bracket	Tax Rate
0 – 50,000 SSP per month	0%
50,001 – 150,000 SSP per month	5%
150,001 – 300,000 SSP per month	10%
300,001 – 600,000 SSP per month	15%
Above 600,000 SSP per month	20%

Pension in South Sudan

Formal, nationwide pension schemes in South Sudan are still developing, and many private-sector employers rely on contractual end-of-service benefits or private savings arrangements instead of statutory pension funds. Larger employers sometimes offer voluntary pension or provident fund contributions through regional or international providers, which should be clearly documented in employment contracts and company policies.

Managing Common Payroll Challenges in South Sudan

Global employers operating in South Sudan often encounter unique payroll challenges that can affect compliance and efficiency, like navigating evolving tax laws and managing employee data. With a need for real-time accuracy, modern organizations must develop strategies to overcome these challenges effectively. Below, we explore some of the most common payroll hurdles and provide actionable solutions to streamline payroll processes in South Sudan.

Maintaining Accurate And Detailed Payroll Reports

Maintaining accurate global payroll reports is often challenging due to currency exchange complexities, data integration issues, and the need to keep employee information up-to-date –including tax information, hours worked, leave balances, and any changes in salary or job status. Generating accurate reports is easy with a comprehensive payroll automation tool that consolidates fragmented data sources, and can keep track of employee payments and deductions.

Keeping up with ever-changing tax laws & Compliance Laws

In South Sudan, tax laws and compliance regulations can change frequently, presenting a significant challenge for global employers. Monitoring updates to federal, state, and local tax codes is crucial to avoid non-compliance and costly penalties, but requires significant time and resources. Partnering with local experts or a reputable global HR platform is an effective way to maintain compliance. These services can help employers stay compliant with evolving regulations while freeing up time for more strategic work.

Consolidating Multi-Vendor Payroll Analytics

Managing payroll across multiple vendors often leads to fragmented data and inefficiencies, making it difficult to consolidate analytics. These challenges can hinder decision-making, especially when trying to gain a clear view of workforce costs and trends. To address this, organizations can invest in a centralized payroll management system that unifies data from multiple vendors. A consolidated platform simplifies payroll tracking, ensures data accuracy, and provides actionable insights into payroll expenditures.

Integrating Multiple HR & Payroll Systems

Global companies are prone to using multiple HR or payroll systems across regions, which can easily lead to fragmented payroll data, increasing the risk of delays and errors in employee compensation. To combat this, seamless integration between payroll and other systems is critical.

Payroll management systems that connect with existing HR and financial platforms can help streamline workflows by reducing manual inputs and ensuring that all departments operate with up-to-date, accurate information. In turn, this helps guarantee on-time, accurate payroll, boosting employee satisfaction.

How Playroll Can Streamline Payroll & Taxes In South Sudan

Expanding globally is an exciting milestone for any company, but it comes coupled with complex payroll challenges. It doesn’t have to be complicated. At Playroll, our easy-to-implement global payroll management software combines automation with hands-on support to make global payroll truly simple. Here's how Playroll helps:

Multi-Vendor Integration: Our platform syncs seamlessly with your providers and in-house systems to unify global payroll services in one platform.
Standardize Payroll Processes: Unify your operations in one dashboard to ensure payroll is running smoothly globally, with advanced approval flows and reports.
Improve Governance & Compliance: Improve compliance by centralizing all your compliance tasks and processes. Easily track your payment obligations, with digitized audit trails.
Advanced Reporting: Access and configure your data, your way, with a comprehensive suite of payroll analytics and reporting tools.

Disclaimer

THIS CONTENT IS FOR INFORMATIONAL PURPOSES ONLY AND DOES NOT CONSTITUTE LEGAL OR TAX ADVICE. You should always consult with and rely on your own legal and/or tax advisor(s). Playroll does not provide legal or tax advice. The information is general and not tailored to a specific company or workforce and does not reflect Playroll’s product delivery in any given jurisdiction. Playroll makes no representations or warranties concerning the accuracy, completeness, or timeliness of this information and shall have no liability arising out of or in connection with it, including any loss caused by use of, or reliance on, the information.

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