How SHA eClaims Work for Kenyan Hospitals
SHA eClaims Kenya facilities now depend on isn’t optional infrastructure. It’s the only route to getting paid. Since the Social Health Authority replaced NHIF on 1 October 2024, every accredited hospital, clinic, and health centre in the country has had to submit claims through SHA’s digital claims system to receive reimbursement.
As of mid-2026, SHA has contracted over 11,034 health facilities. More than 31 million Kenyans have registered as beneficiaries. The system has paid out over KES 147 billion in claims since the transition began.
If your facility’s billing team is still treating eClaims as a black box where invoices go in and payments occasionally come out, this guide walks through exactly what happens at each stage, and where the process most often breaks down.
Want your HMIS properly connected to SHA’s eClaims system? Book a free SHA integration assessment via WhatsApp – we’ll review your current setup and show you exactly what’s manual today that shouldn’t be.
What Is the SHA eClaims System?
SHA eClaims Kenya-wide runs through the official SHA Provider Portal at portal.sha.go.ke. This is the only authorised platform for facilities to verify patient eligibility, request pre-authorisation, submit claims, and track reimbursement. It replaced the old NHIF claims process entirely.
The portal serves as the single gateway for all three of SHA’s funds: the Primary Healthcare Fund (PHCF), the Social Health Insurance Fund (SHIF), and the Emergency, Chronic and Critical Illness Fund (ECCIF).
For facilities entering claims manually, the portal itself is the interface. For facilities with an integrated Hospital Management Information System (HMIS), the same underlying claims exchange happens automatically in the background through a set of APIs published by the Digital Health Agency (DHA) via its AfyaLink integration hub. These use the international FHIR healthcare data standard.
Both routes end up in the same place: a claim submitted to SHA for adjudication. However, the difference lies in how much manual re-typing your billing staff have to do to get there, and how much visibility you have while a claim is in progress.
The SHA eClaims Process, Step by Step
1. Facility Contracting (e-Contracting)
Before submitting any claim, a facility must complete accreditation and e-contracting with SHA. This requires a valid KMPDC practice licence, a county health facility licence, a KRA PIN, and completed bank details. You must upload and verify all of these through the provider registration process on the portal. Only facilities that complete this step receive login credentials. Without them, you cannot submit any claim at all.
2. Real-Time Patient Eligibility Verification
Before treatment begins, reception staff must verify that the patient’s SHA cover is active. This happens in real time, either through the portal, via the *147# USSD code, or through an OTP sent to the member’s phone. For facilities using an integrated HMIS, this same check happens automatically against SHA’s client registry the moment a patient’s SHA number is entered. Skipping this step is one of the most common and costly mistakes facilities make. SHA cover lapses when contributions aren’t up to date, and a facility that treats an inactive member absorbs that cost itself.
3. Checking Whether the Intervention Requires Pre-Authorisation
Every benefit under SHA’s tariff schedule is flagged Y or N for whether it requires pre-authorisation before treatment starts. Routine outpatient consultations typically don’t. Planned surgeries, dialysis, and a range of higher-cost interventions typically do. Skipping this check is how facilities end up with the retrospective pre-authorisation rejections that have become a well-documented pain point for hospital administrators.
4. Submitting the Pre-Authorisation
Where pre-authorisation is required, the facility adds the diagnosis, attaches supporting documents (ID, referral notes, or other justification), and submits the request before the visit proceeds. On the technical side, the system submits this as a FHIR claim bundle with its use flagged as “preauthorization.” It carries the patient, practitioner, facility, and diagnosis details together in one structured message. The facility then waits for SHA’s approval before proceeding, except in genuine emergencies.
5. Service Delivery and Clinical Coding
Once treatment is delivered, every intervention needs coding correctly on two fronts: a valid ICD-11 diagnostic code, and the matching SHA intervention code (for example, a code in the SHA-08 or SHA-16 series for a specific procedure or service). This dual coding requirement represents a genuine shift from the ICD-10 codes many facilities used under NHIF. Mismatched or missing codes rank among the most common causes of claim rejection.
6. Submitting the Claim Within 7 Days
This is the hard deadline. You must submit claims electronically within 7 days of the date of service or discharge. On the portal, this means entering the invoice number generated by the facility’s own billing system, adding each invoice line against the correct claim intervention bill item, attaching the diagnosis, and uploading supporting documents typically a scan of the invoice, the prescription, and the signed claim form before reviewing and submitting. For integrated facilities, the equivalent claim is submitted automatically as a structured FHIR bundle the moment a patient is discharged and billed. Miss the 7-day window, and SHA’s system automatically flags the claim. A repeated pattern of late submissions can also trigger a fraud review.
7. Claim Adjudication and Status Tracking
Once submitted, a claim moves through a defined set of states. Facilities can track these via the portal’s claims history, or via a status-tracking API for integrated systems. Claims queue for processing, then either receive approval or rejection. They may be routed to in-review or clinical-review if they need closer scrutiny. From there, approved claims move to payment processing, while claims showing unusual patterns may be flagged for surveillance. Furthermore, facilities should follow up in writing if a submitted claim shows no decision after 30 days.
8. Payment and Reimbursement
SHA’s stated target is to pay approved claims within 7 days of submission. In practice, this target is met inconsistently. Primary Healthcare Fund claims have reportedly had their processing timeline cut from 90 days to 30 days. However, inpatient, surgical, renal, and cancer-related claims under SHIF and ECCIF have seen significant backlogs. Private hospitals were owed tens of billions of shillings in unpaid claims as of mid-2026. Consequently, understanding where your specific claim sits in this process is exactly why status tracking matters as much as submission itself.
Manual Portal Entry vs. Integrated HMIS Submission
Every facility has a choice in how it interacts with the SHA eClaims system.
Manual portal entry means a staff member logs into portal.sha.go.ke directly. They re-type the invoice details, diagnosis, and bill items by hand. They upload scanned documents one claim at a time. It works, and for a very small facility with low patient volumes, it may be manageable. However, it is inherently slower and more prone to transcription errors. Moreover, it gives staff no way to see claim status changes without manually checking each one.
Integrated HMIS submission means the facility’s own patient management, billing, and clinical systems talk directly to SHA’s claims APIs through the DHA’s AfyaLink integration layer. Eligibility checks, pre-authorisation requests, and claim submissions happen automatically from data already captured during the patient’s visit, with no re-typing. Claim status updates flow back into the same system facility staff already use daily, rather than requiring a separate portal login and manual check.
For any facility handling more than a handful of claims a day, the integration route removes the exact failure points that drive most rejections: transcription mismatches, missed submission windows because claims queued for manual entry, and coding inconsistencies between what a clinician documented and what actually got billed.
Where This Connects to Claim Rejections
Nearly all of the process above is designed to prevent the same failure points we’ve covered in detail separately: missing documentation, missed the 14-day resubmission window on returned claims, mismatched pre-authorisation references, and coding errors.
If your facility is losing revenue specifically to rejections rather than to the eClaims process itself, our guide on why SHA claims get rejected and how to reduce rejections breaks down the real numbers behind each cause and a practical system for cutting your rejection rate.
The Bottom Line
SHA eClaims Kenya-wide is a genuinely more structured process than the old NHIF claims system: verified eligibility, coded diagnoses, tracked status, defined payment timelines. However, structure only helps if your facility’s own workflow matches it. Whether you’re submitting manually through the portal or through an integrated HMIS, the same eight steps apply: contracting, eligibility verification, pre-authorisation where required, correct coding, timely submission, status tracking, and payment. Consequently, facilities that treat each step deliberately, rather than as an afterthought bolted onto existing billing habits, are the ones seeing claims move smoothly from submission to payment.
Get Your HMIS Properly Connected to SHA eClaims
Manually re-entering claims on the SHA portal is exactly how facilities end up with the coding errors, missed deadlines, and documentation gaps that drive rejections. Our managed IT services for healthcare facilities team helps hospitals and clinics integrate their HMIS directly with SHA’s eClaims APIs, so eligibility checks, pre-authorisation, and claim submission happen automatically instead of manually.
For related reading, see our guides on why SHA claims get rejected and how to reduce rejections and the full SHA HMIS integration guide for Kenyan hospitals.
Want a free assessment of your facility’s SHA eClaims setup? Book it via WhatsApp or visit Sapiens IT Lab to request a full on-site review – we’ll show you exactly where manual entry is costing you time and revenue.
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