LHDN e-invoice software for clinics in Malaysia (MyInvois)

Honest scope. This page explains how LHDN e-invoice applies to clinics and where Desk Clinic is on the roadmap. It is not legal or tax advice. Verify your specific phase-in date and technical specifications on the official LHDN MyInvois portal, and consult your accountant before go-live.

What LHDN e-invoice (MyInvois) actually requires

MyInvois is run by the Inland Revenue Board of Malaysia (LHDN / IRBM). Every taxable supply must be submitted as a structured electronic invoice (UBL 2.1 JSON), validated by LHDN, and returned with a Unique Identifier Number (UUID), Long ID, and a QR code that must be embedded on the copy delivered to the buyer. Both buyer and seller have a 72-hour window to reject or cancel the document; after that, only a credit note can adjust it.

For clinics, the submission must include supplier identifiers (TIN, BRN/SSM number, MSIC industry code, SST registration where applicable, registered address with state code) and buyer identifiers (TIN for B2B; for unprompted B2C walk-ins, a generic buyer TIN can be used in a consolidated submission). Each line item carries a description, an LHDN classification code, quantity, unit price, tax type, tax rate, and tax amount.

Who must comply, and when

Compliance is phased by annual turnover. Larger healthcare groups have already gone live; smaller private clinics fall into later phases. Phase dates have been revised more than once, so the only authoritative answer is the current schedule on the LHDN MyInvois portal. Two things that don't change: there is no opt-out, and when your phase begins, every taxable invoice the clinic issues must be reflected in MyInvois (individually or via the monthly consolidated B2C submission).

How LHDN e-invoice works for a clinic visit

A typical day at a private clinic produces three kinds of patient encounters that need different MyInvois treatment:

• Walk-in B2C, no e-invoice requested: Issue your usual receipt at the counter, then aggregate all such visits into one consolidated B2C e-invoice submitted to LHDN by the 7th of the following month. The patient never sees the MyInvois QR code—their receipt is unchanged.
• Walk-in B2C, patient requests an e-invoice: Capture the patient's TIN (and BRN/SSM for sole proprietors) at billing, submit an individual e-invoice in real time, and print or email the invoice with the validated QR code. Do this on demand—every patient has the right to request one.
• B2B / corporate panel / TPA insurance: Always submit an individual e-invoice with the buyer's TIN, BRN, and address. These cannot be consolidated. This is the most common case for clinic panel billing in Malaysia and where TPA reconciliation gets thorny without a unified billing record.

Refunds and corrections within the 72-hour window can use cancellation; beyond that, you must issue a credit note e-invoicelinked to the original. Foreign patients without a Malaysian TIN are handled with a generic LHDN-issued TIN (currently EI00000000010) and their passport number.

What your clinic software needs to handle

An LHDN-compliant clinic software stack needs to cover seven things end to end—not just "submit invoice":

• Supplier profile per organization: TIN, BRN/SSM, MSIC code, SST registration, registered address, contact—stored on file and signed into every submission.
• Buyer capture at billing: Prompt for TIN at the point of payment if the patient asks for an e-invoice; remember it on the patient record so repeat visits don't re-enter.
• Item classification: Each invoice line carries an LHDN classification code (consultation vs procedure vs medicine vs consumable) and a SST treatment (exempt vs taxable vs zero-rated).
• Submission and status tracking: Submit to LHDN's API, store the returned UUID + Long ID, and reflect validation status (Submitted, Valid, Cancelled, Rejected) on the invoice.
• QR code on the invoice copy: Embed the validation QR on the printed or emailed invoice so patients can verify authenticity on the LHDN portal.
• Cancellation and credit-note workflow: Honour the 72-hour rejection/cancellation window with one-click cancellation and a credit-note generator linked to the original UUID.
• Consolidated B2C batching: Aggregate all unprompted walk-in receipts and submit one consolidated e-invoice by the 7th of the following month—automatically, not manually.

Desk Clinic's roadmap (honest)

LHDN e-invoice integration is on our roadmap. Here is exactly where we are:

• What's already in place: The Invoice and Payment data model already supports line items in cents, tax fields, currency, place of supply, patient (buyer), and organization (supplier). We track invoice status (draft → issued → paid → void) and have an InsuranceClaim precedent for asynchronous external submission with status callbacks—the same pattern MyInvois needs.
• What we're scoping: Certified-middleware integration (so we don't depend on LHDN sandbox approval for every customer), supplier-profile fields per organization, item-level LHDN classification, automated B2C consolidated submission, QR-on-PDF rendering, and credit-note workflow.
• How we're approaching it: Middleware-first MVP for clinics already in their phase, with a path to direct LHDN integration once volume justifies the operational cost. No customer will need to migrate data when we switch on.

If your clinic is approaching its phase-in date and you would like to join the early-access group, please contact us.

How to prepare your clinic now

Whether you choose Desk Clinic or another vendor, these steps reduce go-live risk:

• Confirm your phase-in date and turnover band on the official LHDN MyInvois portal—don't rely on third-party summaries.
• Register your clinic on the MyInvois portal and get API credentials (or contract a certified middleware provider).
• Capture supplier fields on file: TIN, BRN/SSM, MSIC industry code, SST registration, and the registered address with state code.
• Decide your B2C consolidation policy: prompt every walk-in for a TIN, or default to consolidated and only collect TIN on request.
• Standardize item classification on your fee schedule—consultations, procedures, medicines, and aesthetic services need different classification codes and SST treatment.
• Plan your TPA / corporate panel workflow: B2B individual e-invoices are mandatory and you'll need buyer TIN/BRN for every panel customer in your master list.

Use our Malaysia clinic compliance checklist (Section 6 covers e-invoice readiness) as a printable starting point.

Related Malaysia resources

• Malaysia clinic management system hub — overview and links to every Malaysia-related page.
• Clinic management system Malaysia (solution deep dive)
• Malaysia compliance checklist (MOH, PDPA, LHDN e-invoice, records)
• Clinic billing software & medical billing system — the underlying invoicing and payment workflow.
• Kreloses vs Desk Clinic — competitor comparison for Malaysia buyers.

Get started

Start a free trial to use Desk Clinic for scheduling, records, and billing today, and contact us to be notified when LHDN e-invoice integration ships. You can also view pricing.