How To Clear Pending KRA Penalties

Taxpayers need to clear pending KRA penalties to maintaining a clean tax record and obtaining a Tax Compliance Certificate (TCC). As of 2026, the Kenya Revenue Authority (KRA) has introduced more automated tools like the Automated Payment Plan (APP) to help taxpayers manage these liabilities.

The first Step to clear pending  KRA penalties one needs to Check for Pending Penalties

Before paying, you must identify exactly what you owe and for which period.

1. Log in to the KRA iTax Portal using your PIN and password.
2. Navigate to the ‘My Ledger’ tab and select ‘General Ledger Report’.
3. Select your Tax Obligation (e.g., Income Tax-Resident Individual) and click ‘Show Ledger’ to view specific penalties and interest

To clear pending KRA penalties and restore your tax compliance status, you can choose from three main paths depending on your financial situation and the nature of the debt.

Option 1: Direct Payment (Fastest Method)

Use this if you can pay the full penalty immediately.

1. Log in to iTax: Access the KRA iTax Portal using your PIN and password.
2. Generate a PRN: Navigate to ‘Payments’ > ‘Payment Registration’.
3. Select Details: Choose the Tax Head (e.g., Income Tax) and select ‘Penalty & Interest’ as the Tax Sub-head.
4. Submit & Pay: Generate the Payment Registration Number (PRN). Pay via M-Pesa using PayBill 222222 with the PRN as your account number.

Option 2: Automated Payment Plan (APP) 

Introduced in late 2025, this allows you to pay off total liabilities in instalments.

1. Navigate to Debt Tab: On iTax, select the ‘Debt and Enforcement’ menu.
2. Apply for APP: Click on ‘Apply for Automated Payment Plan’.
3. Propose Schedule: The system will display your confirmed debt. You can propose a payment schedule for up to 6 months.
4. Approval: Most applications are approved automatically by the system if you meet eligibility criteria.

Option 3: Request a Waiver of Penalty & Interest 

You can apply to have penalties removed if they were erroneous or due to circumstances beyond your control.

1. Pay Principal First: You cannot get a waiver on the principal tax; this must be fully paid before applying.
2. Apply on iTax: Go to ‘Debts and Enforcement’ > ‘Request for Waiver of Penalties and Interests’.
3. Provide Evidence: You must upload a formal letter and supporting documents (e.g., proof of student status or system errors) explaining why you deserve the waiver.
4. Wait for Review: KRA will notify you of their decision via your registered email.

Key Compliance Deadlines (2026)

• Amnesty: Note that the major tax amnesty window for debts prior to 2023 generally closed on June 30, 2025.
• Validation: Starting January 1, 2026, KRA began validating all income tax returns against eTIMS and customs data to automatically flag discrepancies.

How to download your KRA Ledger

If you’re unsure of your exact debt you need to download your KRA Ledger for a clear breakdown.

To download your KRA ledger and see a full breakdown of your tax position, follow these steps on the iTax portal:

Step 1: Access the Ledger Report

1. Log in to your iTax account using your KRA PIN and Password.
2. On the top menu, hover over the ‘My Ledger’ tab.
3. Click on ‘General Ledger Report’.

Step 2: Filter for Specific Data

1. Select Tax Obligation: From the dropdown, choose the specific tax you want to check (e.g., Income Tax – Resident Individual or VAT).
2. Select Account Type: Usually, this is set to “Taxpayer Main Account.”

1. • Note: If you are looking for older records from before iTax was fully implemented, select ‘Taxpayer Legacy Account’.
2. Choose Date Range: Select the ‘From Date’ and ‘To Date’ for the period you wish to review.

Step 3: View and Download

1. Click the ‘Show Ledger’ button.
2. The system will display a summary of your transactions, including payments, return assessments, and penalties.
3. To save a copy, click the ‘Download’ button (usually in Excel or PDF format) at the bottom or top of the report list.

Alternative: Debt & Enforcement Tab

For a more detailed statement specifically focused on outstanding balances and migrated legacy data, navigate to the ‘Debt & Enforcement’ menu and select ‘Detailed Statement’.

If you find discrepancies in your ledger, you can contact your Tax Service Office (TSO) to request a formal reconciliation