A company PIN on its own does not make you an employer in KRA’s eyes. Most of the trouble I see with new payrolls starts there: the business hires its first person, pays them, and only discovers in the third month that iTax won’t take a PAYE return because the obligation was never added. Sort out the registrations below before the first salary leaves the bank, not after.
What you register, and where
| Registration | Where | When it matters |
|---|---|---|
| Income Tax PAYE obligation on your PIN | iTax | From the month you first pay an employee |
| NSSF employer number | NSSF employer self-service portal | From the first payroll |
| SHA employer account | SHA employer portal (employers.sha.go.ke) | From the first payroll |
| NITA | National Industrial Training Authority | Levy is declared on the PAYE return |
| HELB | HELB employer portal | Only when you employ someone with a HELB loan |
The Affordable Housing Levy has no separate registration. It sits inside the PAYE return and is paid through iTax, so getting the PAYE obligation right covers it.
The PAYE obligation on iTax
Log in to iTax with the company PIN, go to Registration, then Amend PIN Details, and use the online form. Under the obligation details, add Income Tax - PAYE and give the effective date. Use the date you first hired or first paid staff, not the date you happen to be filling in the form. KRA reviews the request and the obligation becomes active only once an officer approves it, so allow a few days.
Two practical points:
- Once the obligation is active, a return is due every month, even a month with no staff. The penalty for a late PAYE return is the higher of 25% of the tax due or KES 10,000, and on a nil return the higher figure is always the KES 10,000. Dormant companies with an old PAYE obligation collect these penalties quietly for years.
- If you have branches with their own PINs, decide early which entity is the employer. The simplified return asks whether you are filing as head office or branch.
NSSF
Register the business as an employer on the NSSF self-service portal and you will get an employer number used on every monthly schedule. Contributions are due by the 9th of the following month.
Since 1 February 2026 the Year 4 limits apply: 6% from the employee and 6% from the employer, on pensionable pay with a lower earnings limit of KES 9,000 and an upper earnings limit of KES 108,000. The most either side pays is KES 6,480 a month. See NSSF Year 4 explained.
SHA (SHIF)
SHIF replaced NHIF in October 2024. Employers register on the SHA employer portal with the company’s KRA PIN and business registration documents. If you were an NHIF employer, the portal pulls your old record and asks you to confirm it.
The employee pays 2.75% of gross pay, with a minimum of KES 300. There is no employer contribution. Remittance is due by the 9th of the following month under the 2024 regulations. More detail is in SHIF for employers.
NITA
The industrial training levy is KES 50 per employee per month, paid by the employer and not deducted from staff. Register the business with NITA. The levy itself is now declared on the PAYE return: the simplified return counts the employees on the employee sheet and multiplies by KES 50, and you pay it to KRA on a separate payment slip. Confirm with NITA whether your business qualifies for any first-year exemption before you rely on one.
HELB
You don’t register with HELB until you employ a loan beneficiary. When you do, notify HELB and start deducting what it asks. HELB says employers must notify it within three months of employing a beneficiary, and deductions are due by the 15th of the following month. Ask every new hire whether they have a HELB loan; most people will tell you if you ask, and almost nobody volunteers it.
What to collect from each employee
Have these on file before you run the first payroll:
- KRA PIN with an income tax obligation. The simplified PAYE return rejects a PIN that has no income tax obligation. Check each PIN on iTax or the KRA PIN checker when the person joins.
- National ID or passport number.
- NSSF number, and SHA registration (the SHA number is usually the ID number).
- Bank or M-Pesa details for net pay. See paying salaries by M-Pesa or bank.
- Insurance premiums, pension, mortgage or PRMF details if they want the reliefs; ask for the policy or interest certificate now, not in February.
- Whether they have another job. Personal relief goes with the main employment only.
The Employment Act requires a written contract for anyone employed for three months or more. Check the pay against the gazetted minimum wage for the role and location.
Work injury cover under the Work Injury Benefits Act is also a legal requirement for employers. It is arranged with an insurer rather than through payroll, but put it on the same checklist.
The first month, worked through
Say you hire one person on a basic salary of KES 65,000 and pay July 2026 salary on 31 July. Under the rules in force from 1 July 2026, the payslip and employer cost look like this:
| Item | KES |
|---|---|
| Gross pay | 65,000.00 |
| NSSF employee (Tier I 540.00 + Tier II 3,360.00) | 3,900.00 |
| SHIF | 1,787.50 |
| Housing Levy, employee | 975.00 |
| PAYE after personal relief of 2,400 | 9,884.60 |
| Net pay | 48,452.90 |
| NSSF employer | 3,900.00 |
| Housing Levy, employer | 975.00 |
| NITA | 50.00 |
| Total employer cost | 69,925.00 |
Then the deadlines for that July payroll:
| What | Due |
|---|---|
| PAYE return and payment, NITA declared on the same return | 9 August 2026 |
| NSSF | 9 August 2026 |
| SHIF | 9 August 2026 |
| Housing Levy (9th working day) | 13 August 2026 |
| HELB, if any | 15 August 2026 |
9 August 2026 is a Sunday. Don’t count on the weekend buying you time; file and pay on the Friday before.
If a registration isn’t through by the first deadline, deduct anyway, keep the money aside and file as soon as the account is live. Not deducting is a separate offence under the Income Tax Act, with a penalty of 25% of the tax involved or KES 10,000, whichever is higher.
Run your own figures through the free net pay calculator, and keep the filing calendar open for the dates.