KRA eTIMS for Pharmacies: What You Need to Do
Pharmacy & Compliance · 6 min read · Updated 2026-06-26
KRA's electronic Tax Invoice Management System (eTIMS) changed how every VAT-registered business in Kenya issues invoices, and pharmacies are squarely in scope. The rules are not complicated, but getting the workflow wrong means rejected expense claims for your customers and compliance risk for you. Here is the practical version.
What eTIMS actually is
eTIMS is KRA's system for capturing tax invoices electronically in real time. Instead of issuing a paper receipt that only you have a record of, a compliant invoice is transmitted to KRA and stamped with a control unit identifier and a QR code. The goal is simple from KRA's side: every taxable sale is visible as it happens.
Does it apply to your pharmacy?
If your pharmacy is VAT-registered, yes, your sales invoices need to be eTIMS-compliant. Even where many drugs are zero-rated or exempt, the invoice itself still has to go through the system with the correct tax classification per line item. "We mostly sell exempt items" is not an exemption from issuing compliant invoices.
What a compliant invoice must carry
- Your KRA PIN and the customer's PIN (for B2B sales where the buyer wants to claim)
- Correct tax classification per item (standard-rated, zero-rated, or exempt)
- The eTIMS control unit number and QR code
- Date, time, and a unique invoice number
The per-line tax classification is where pharmacies trip up: a single basket can mix standard-rated, zero-rated, and exempt items, and each must be coded correctly.
How it works at the counter
In practice, compliance should be invisible to your dispenser:
- The sale is rung up at the POS as normal
- Each item already carries its correct tax classification
- On completion, the invoice is transmitted to eTIMS automatically
- The receipt prints with the KRA QR code and control number
If your team has to re-enter the sale into a separate KRA portal, you have the wrong setup, that double entry is slow and error-prone, and it is where compliance breaks down on a busy day.
Common mistakes that cause problems
- Treating eTIMS as an end-of-day batch job instead of per-invoice
- Wrong tax classification on items, so customers can't claim correctly
- No customer PIN captured on B2B sales that need it
- Relying on manual entry into the KRA portal alongside the POS
How AfyaConnect keeps pharmacies compliant
AfyaConnect's pharmacy POS is built for KRA eTIMS. Each product carries its tax classification, invoices are transmitted with the control number and QR code, and the compliant receipt prints at the counter, no separate portal, no double entry. Combined with the PPB controlled substances register and M-Pesa billing, your counter handles tax, compliance, and payment in one flow.
If eTIMS is slowing down your queue or creating reconciliation headaches, register your pharmacy and see compliant invoicing built into the POS.