How to File a BIR VAT Refund Claim: The 90-Day Processing Rule Explained

A BIR VAT refund claim for unutilized input tax must be decided by the Bureau of Internal Revenue within ninety (90) days from the date the taxpayer submits complete supporting documents, under Section 112(C) of the National Internal Revenue Code (NIRC) as amended by the TRAIN Law. If the BIR denies the claim in whole or in part, the taxpayer has 30 days from receipt of that decision to appeal to the Court of Tax Appeals (CTA) — the same 30-day window also applies if the 90 days simply lapse without any BIR action.

This guide covers the current 90-day rule, how it differs from the older 120+30 day framework, the EOPT Act’s risk-based claim classification, and a worked example for an exporter tracking the clock on a refund claim.

What is the current 90-day VAT refund rule? #

Under Section 112(C) of the NIRC, as amended by the TRAIN Law (Republic Act No. 10963), the Commissioner of Internal Revenue must grant or deny a VAT refund claim for unutilized input tax within ninety (90) days from the date the taxpayer submits the official receipts, invoices, and other documents supporting the application. The TRAIN Law took effect January 1, 2018, and Revenue Regulations No. 26-2018 (issued December 27, 2018, amending RR No. 13-2018) clarified that the 90-day clock runs from the filing of a complete claim — meaning the date the taxpayer submits all required supporting documents, not merely the date the application is first lodged — through to the actual release of the refund payment, and confirmed that applications filed from January 1, 2018 onward are covered by the 90-day period.

This 90-day period replaced the 120-day period that applied to VAT refund claims before the TRAIN Law’s amendment — the same 120-day period at issue in the Supreme Court’s CIR v. San Roque Power decision (see the historical framework below).

What happens if the BIR doesn’t act within 90 days? #

Missing the 90-day deadline does not automatically grant the refund. RR No. 26-2018 states that if the 90-day period lapses without the refund being released, the claim may continue to be processed administratively — the clock running out does not itself convert a pending claim into an approved one. What the deadline does trigger is accountability and a taxpayer remedy:

• BIR accountability: any official, agent, or employee of the BIR who fails to act on a VAT refund application within the 90-day period is subject to criminal penalties under Section 269 of the NIRC, including fine, imprisonment, and perpetual disqualification from public office upon conviction.
• Taxpayer’s appeal right: under the Ease of Paying Taxes (EOPT) Act (Republic Act No. 11976), which took effect January 22, 2024, the taxpayer has 30 days from the lapse of the 90-day period (with no BIR action) to appeal to the CTA — restoring an explicit appeal right that had become uncertain after the TRAIN Law’s amendment. Do not assume a refund is deemed granted simply because 90 days have passed; the safer reading of the current rule is that inaction preserves the taxpayer’s right to escalate, not that it automatically pays out the claim.

What if the claim is denied? #

A full or partial denial gives the taxpayer 30 days from receipt of the BIR’s written decision to appeal to the Court of Tax Appeals. The BIR must state the legal and factual basis for any denial. This 30-day appeal window is the same length whether the trigger is an actual denial letter or the 90-day period lapsing without action — the taxpayer should calendar both possible start dates (denial receipt, or day 91 of silence) and file the CTA petition within 30 days of whichever occurs.

How does the EOPT Act’s risk-based classification affect processing? #

Since Revenue Regulations No. 5-2024 took effect for claims filed beginning July 1, 2024, the BIR sorts every VAT refund claim into low, medium, or high risk before deciding how much of it to verify — but the 90-day decision deadline itself did not change. Classification depends on factors such as the amount of the claim, the taxpayer’s filing frequency, and compliance history:

First-time claimants are automatically classified high risk for their first four claims, and a taxpayer with three consecutive low-risk claims is subject to mandatory full verification on the fourth claim regardless of classification. All claims — regardless of risk tier — still require complete supporting documentation from the outset; the classification affects how much the BIR checks, not whether the 90-day period applies.

Required supporting documents #

A VAT refund claim generally needs, at minimum:

• Sales invoices and official receipts supporting the VAT-exempt, zero-rated, or excess input tax position claimed
• Purchase invoices and official receipts supporting the input VAT being refunded
• Proof that zero-rated sales qualify as such — for exporters, this includes proof of shipment and proof of inward remittance of export proceeds in acceptable foreign currency accounted for under Bangko Sentral ng Pilipinas rules (see VAT Zero-Rating for Exporters for the current export-ratio certification requirements)
• Summary schedules reconciling the claimed input tax to the VAT returns filed for the period
• Any additional documents the BIR requests during verification, particularly for claims classified as medium or high risk

The 90-day clock does not start until the taxpayer has submitted a complete set of these documents — an incomplete initial filing means the claim isn’t yet “filed” for purposes of the 90-day count under RR No. 26-2018.

How is this different from the old 120+30 day rule? #

The current 90-day rule is the direct descendant of the 120-day rule at the center of the Supreme Court’s landmark CIR v. San Roque Power decision — the arithmetic changed, but the mandatory-and-jurisdictional character of the deadline did not. Before the TRAIN Law, Section 112(C) gave the BIR 120 days to decide a claim, followed by a 30-day appeal window; the Supreme Court held in that case that both periods were mandatory and jurisdictional, meaning a judicial petition filed outside those windows left the CTA without power to hear the case at all, regardless of whether the underlying refund was valid. For the full background on that ruling — including why three companies with similar claims got three different outcomes, and the narrow BIR-ruling reliance exception that saved one of them — see CIR v. San Roque Power: Why the 120+30 Day VAT Refund Rule Is Mandatory and Jurisdictional. Treat that post as historical background on how strictly courts enforce this deadline — the number of days it discusses (120+30) is no longer the applicable rule for claims filed today; use the 90+30 day structure in this guide instead.

Worked example: an exporter tracking the 90-day clock #

A garments exporter accumulates ₱1,200,000 in unutilized input VAT for the four quarters of 2025, attributable to purchases supporting its zero-rated export sales under NIRC Section 106(A)(2). In February 2026, it prepares its administrative claim:

If the claim is classified low risk because the exporter has a clean multi-year compliance history and modest claim size relative to its sales, the BIR may process it without further sales/purchase verification. If classified medium or high risk — for example, because it is the exporter’s first claim — the BIR verifies 50% to 100% of the underlying transactions before the 90-day deadline, which is exactly why complete, well-organized documentation from day one matters more under the current risk-based system than it did before.

Frequently asked questions #

How many days does the BIR have to decide a VAT refund claim? #

Ninety (90) days from the date the taxpayer submits complete supporting documents, under Section 112(C) of the NIRC as amended by the TRAIN Law (Republic Act No. 10963) and clarified by Revenue Regulations No. 26-2018. This replaced the earlier 120-day period that applied before the TRAIN Law’s amendment.

Is a VAT refund automatically granted if the BIR misses the 90-day deadline? #

No. If the 90-day period lapses without the BIR releasing the refund, the claim is not automatically granted — it may continue to be processed administratively, and any BIR official, agent, or employee who fails to act within the period is subject to penalties under Section 269 of the NIRC. The taxpayer’s separate remedy is a 30-day window to appeal to the Court of Tax Appeals after the 90 days lapse.

What can a taxpayer do if the BIR denies a VAT refund claim? #

The taxpayer may appeal a full or partial denial to the Court of Tax Appeals within 30 days from receipt of the decision. The same 30-day appeal window applies if the BIR simply fails to act within the 90-day period, running from the lapse of that period.

How is the current 90-day rule different from the old 120+30 day rule? #

Before the TRAIN Law, Section 112(C) gave the BIR 120 days to decide a VAT refund claim, followed by a 30-day appeal window, as applied in CIR v. San Roque Power. The TRAIN Law shortened the BIR’s decision period to 90 days starting in 2018, and the Ease of Paying Taxes (EOPT) Act later restored the explicit 30-day appeal right after that period lapses, alongside a new risk-based claim classification system.

What documents are needed to support a VAT refund claim? #

A VAT refund claim must be supported by complete documentation substantiating the input tax being claimed and, for zero-rated sales, proof that the sales qualify for zero-rating — commonly sales invoices, purchase invoices/official receipts, proof of foreign currency inward remittance for exports, and other records the BIR’s risk-based verification process may require depending on whether the claim is classified as low, medium, or high risk under Revenue Regulations No. 5-2024.

Summary #

The BIR must decide a VAT refund claim within 90 days of complete documents under Section 112(C) as amended by the TRAIN Law and RR No. 26-2018 — down from the 120-day period litigated in CIR v. San Roque Power. Missing the deadline does not auto-grant the refund; it opens a 30-day window, restored by the EOPT Act, for the taxpayer to appeal to the CTA, the same window that applies to an outright denial. Since mid-2024, RR No. 5-2024’s risk-based classification determines how much of the claim the BIR verifies, but the 90-day clock and the documentation burden apply to every claim regardless of risk tier. Build the complete file — invoices, proof of zero-rating, and BSP-compliant export remittance proof — before filing, since the 90-day count only starts once the submission is complete.