Complete Guide on How to Apply For KRA Tax Amnesty

Towards the end of 2024, the Tax Procedures (Amendment) Act, 2024 reintroduced the Tax Amnesty program from 27th December 2024 until 30th June 2025, providing eligible individuals and businesses with full waivers on interest, penalties, or fines linked to tax obligations accrued up to 31st December 2023. The primary goal of the program is to support the taxpayers regularise their tax ledgers through corrections or reconciliations and doing away with existing erroneous obligations.

A key point worth noting is that taxpayers who haven’t filed their returns for several years, including nil returns will need to do so before settling the principal tax payments for the amnesty can apply. Filing relevant returns will automatically trigger the system to waive interest and penalties accrued, making one eligible for amnesty without needing another application.

The Tax Amnesty programme applies to all the taxes covered under the Tax Procedures Act, 2015, which includes VAT, PAYE, Income Tax and other obligations that were all due on or before the 31^st of December 2023. The amnesty clears debt from a self-assessment, reconciliation process or a revised return, upon payment of the principal taxes owing.

Exclusions to the program include any penalties, taxes or interests accrued from 1^st January 2024 onwards or other fines that aren’t directly related to a tax debt, such as administrative penalties. The program was initially introduced in 2023. In KRA’s Full Year 2023/2024 performance, the Tax Amnesty programme collected Ksh43.9 billion after 2,617,111 taxpayers were granted amnesty during that financial year.

As of the end of May 2025, over Ksh170 billion in penalties, interest and fines have been waived, with more than 3 million taxpayers benefiting from the amnesty program, demonstrating the program’s wide-reaching impact. This reflects great uptake of the initiative and the program’s success in resolving legacy issues in taxpayer ledgers. While the program has also facilitated the collection of Ksh13 billion in principal tax, the primary emphasis majorly remains on providing relief through correction and waivers to those who qualify.

Who is eligible for Tax Amnesty?

Under the tax amnesty program, there are two main categories for eligible taxpayers.

1. The first category is the taxpayers who do not owe any principal taxes up to the period of 31^st December 2023 but have existing fines, interests or penalties linked to those periods. In this category, the taxpayers automatically qualify, and the systems are automated hence there is no need to apply

1. The second category is for the taxpayers with outstanding principal taxes up to the period of 31^st December 2023. Under this group, one must apply for the amnesty and commit to paying the full outstanding principal, whether in full or in instalments provided it’s cleared by 30^th June 2025.

Taxpayers who also just received new tax assessments or made amendments to past returns after the 31^st of December 2023 are also eligible, provided the period in question is up to 2023’s end. Taxpayers with debts or currently in the dispute process are also eligible but have to engage KRA with a commitment to resolve the matter and agree on the final amounts to be paid before the program elapses.

How to apply for Tax Amnesty

For taxpayers in the second category (Those who need to apply), here are the steps on how to apply.

1. Log in to iTax: Under the Debt and Enforcement menu, select ‘Amnesty Application’. The system will populate the amnesty form with two sections. Section A – confirm your contact information and select the relevant tax obligations. All eligible periods will be auto-selected; uncheck any you wish to exclude. Click ‘Add All’ for each obligation.
2. Set up a payment plan: The added amnesty details shall be populated in Section B. Propose the number of instalments and instalment frequency. The iTax system shall compute the amount per instalment.
3. Submit Application: Click to agree to the terms and conditions and submit. The system will generate an amnesty application acknowledgement with amnesty and payment plan details.
4. Make the Payment: To generate a payment slip, click on the Payment menu and select Payment Registration. Select the Tax head and Sub-head you wish to generate a payment. Click on the radio button and modify the amount to be paid equal to the principal tax.

• Please note: The system will not allow generation of payment with amounts higher than the principal tax due. However, where the principal tax has decimal values, round off the amount to the nearest 1 shilling. Click add, select mode of payment and submit.

1. Receive amnesty Certificate: Once payment has been received, the iTax system shall vacate respective penalties and interest for the period and issue an amnesty certificate.

Key to note is that all payments must be completed by the 30^th June 2025 and the amnesty will only be granted after the final payment is received. Failure to complete the payments within the window, the penalties and interests accrued are no longer eligible for waivers.

Notably, for disputes, taxes or tax assessments, you’ll need to settle the case either through Alternative Dispute Resolution (ADR) or other means before the amnesty can apply.

Whether you’re a business owner, salaried employee, or a large corporation, the tax amnesty program provides an opportunity to correct your tax records, clear past discrepancies, and enjoy peace of mind by avoiding unnecessary penalties or interest. It underscores the government’s commitment to supporting voluntary compliance by offering a clean slate to compliant taxpayers.

Beyond the amnesty, all taxpayers — whether salaried, self-employed, in business, or with no income — are reminded that annual tax filing remains a mandatory obligation. Every registered taxpayer is required to file their returns on iTax by 30th June 2025, regardless of their eligibility for amnesty. Filing returns helps maintain an accurate and up-to-date tax profile, avoids automatic penalties, and demonstrates compliance with the law. Let this be your reminder: file early, file accurately, and stay compliant.