How to Pay GST Online: Challan, Modes, and Receipts

To pay GST online, log in to the official portal at gst.gov.in, generate a payment challan in Form PMT-06 for the exact amount you owe under each tax head, and settle it through net banking, UPI, card, NEFT/RTGS, or a bank counter. The money lands in your Electronic Cash Ledger, and you draw on that ledger when you file your return. The whole flow takes a few minutes once your figures are ready, but the allocation across tax heads has to be right the first time, because moving money between heads later means filing a separate correction form.

What to Have Ready Before You Log In

Three things need to be in front of you when you start: your 15-digit GSTIN, your portal login credentials, and a clear breakdown of what you owe under Central Tax (CGST), State or Union Territory Tax (SGST/UTGST), and Integrated Tax (IGST). Session timeouts are common, and hunting for invoices halfway through the challan will cost you the session.

Work out the figures before you start. You need a summary of your outward supplies, your inward supplies, and any Input Tax Credit you plan to claim, so you can see what has to be paid in cash versus what your credit balance will cover.

Cash Ledger and Credit Ledger: Know the Difference

The portal keeps two virtual accounts for every registered taxpayer, and confusing them is where first-time filers lose money or time.

The Electronic Cash Ledger holds money you deposit through challans. Treat it as a prepaid wallet on the portal. Anything you pay by net banking, UPI, NEFT, card, or at a bank counter goes here first, and you draw on it later to settle tax, interest, penalties, or late fees when you file.¹

The Electronic Credit Ledger holds Input Tax Credit that builds up when you buy goods or services for the business and the supplier has paid GST on them. That credit offsets your output tax directly, so you only deposit cash for the difference. The law requires you to use IGST credit first against IGST liability, then apply any leftover IGST credit against CGST or SGST in either order, before touching your CGST or SGST credit balances.²

Most established businesses end up paying only a fraction of gross liability in cash because ITC covers the rest. The online payment steps below are for that cash portion.

Generating the Challan in Form PMT-06

The challan is where you tell the system how much you want to deposit and against which heads. Log in, go to Services, then Payments, then Create Challan. That opens Form GST PMT-06, which works as a digital deposit slip.¹

The form shows a grid with columns for tax, interest, penalty, late fee, and other amounts, broken out by major head: IGST, CGST, SGST/UTGST, and Cess. Type the rupee figures into the correct cells. If you put ₹5,000 in the CGST interest column when it should have gone under CGST tax, you will need to file Form PMT-09 later to move it.

Once the amounts are in, the portal asks you to pick a payment mode. Once you click “Generate Challan,” the system issues a Common Portal Identification Number (CPIN), a 14-digit tracking code tied to that challan. The challan stays valid for 15 days from the date of generation.¹ If you do not complete payment inside that window, the challan expires and you generate a fresh one.

Choosing a Payment Mode

The portal accepts five payment routes, and the right one depends on your bank, your amount, and how quickly you need the ledger to reflect the deposit.

Internet banking, available through roughly 30 authorised banks integrated with the GST network, including State Bank of India, HDFC Bank, ICICI Bank, Punjab National Bank, and Bank of Baroda.³
UPI or IMPS, usable from any bank. Handy for smaller amounts, or when your bank is not on the net banking list.
Credit or debit card, processed through an authorised bank’s payment gateway.¹
NEFT or RTGS, where the portal produces a mandate form that you take to your bank for a wire transfer. Better for very large amounts.
Over the counter, capped at ₹10,000 per challan per tax period. Print the challan and pay at an authorised bank by cash, cheque, or demand draft.¹

Completing an Internet Banking Payment

Net banking is the fastest option for most taxpayers. After the challan is generated, click Proceed on the summary screen. A dropdown lists every authorised bank. Pick yours, and the browser redirects to your bank’s secure login page.

Sign in with your net banking credentials. Most banks add a second layer, usually an OTP to your registered mobile, before authorising the debit. The bank’s screen shows the exact challan amount. Do not refresh the page or hit back while the bank and portal are talking. If you break the connection, the money can leave your account without immediately showing on the GST portal, and sorting it out then means filing a grievance.

Once you confirm on the bank’s side, the bank signals the GST portal, and you are redirected back to gst.gov.in with a success message. At that point the bank assigns a Challan Identification Number (CIN), an 18-character code that combines a 4-digit bank code with the 14-digit CPIN. The deposit should appear in your Electronic Cash Ledger shortly after.

NEFT, RTGS, and Over the Counter

For NEFT or RTGS, download the mandate form from the portal and submit it to your bank. The bank processes the wire transfer, and the ledger updates once the bank confirms the transaction with the GSTN. That confirmation can take a business day or two, so plan around the return deadline rather than the last hour.

For over the counter, print the challan and take it to an authorised bank branch. Remember the ₹10,000 per challan per tax period ceiling; anything larger has to go through one of the electronic routes.

Confirming the Deposit and Saving the Receipt

Download the paid challan straight after payment. The receipt carries the CIN, the amounts against each head, and the date. Keep a digital and a physical copy. You will want it if a question comes up during audit or when you reconcile your books.

Next, open Services, then Ledgers, and check the Electronic Cash Ledger. The balance should show the deposit. If it does not appear within 24 hours and the amount has not been refunded to your bank, file a grievance in Form GST PMT-07 on the portal.⁴ Do not file before the 24 hours are up; most mismatches clear on their own inside that window as the bank and portal sync.

Once the ledger balance looks right, the deposit can be applied against your liability when you file GSTR-3B. The offset happens inside the return itself, where the system debits both the cash ledger and the credit ledger to cover your tax, interest, and fees for the period.

Fixing Money Posted to the Wrong Head

Depositing money against the wrong head is a common slip: CGST amounts entered in the SGST column, or a tax payment tagged as a penalty. Form GST PMT-09 moves the balance between heads inside your Electronic Cash Ledger without a fresh deposit.⁵

You can shift money between any combination of major heads (IGST, CGST, SGST/UTGST, Cess) and minor heads (tax, interest, penalty, fee, or others) within the same GSTIN. If you hold more than one GSTIN under the same PAN, you can also transfer between GSTINs, but cross-GSTIN transfers are limited to IGST and CGST heads.⁶

To file, go to Services, then Ledgers, then Electronic Cash Ledger, and click the PMT-09 link. Enter the “transfer from” and “transfer to” details, save each record, and file. Verification is by Digital Signature Certificate (DSC) or Electronic Verification Code (EVC) sent to the authorised signatory’s mobile. Companies and LLPs are typically required to use DSC, which needs the EmSigner utility installed and the certificate registered on the portal before you need it; proprietorships and partnerships can use EVC.⁷ Once filed, the ledger updates immediately and you get an Application Reference Number.

Deadlines and What Late Payment Costs

Payment and return filing are linked. GSTR-3B is where liability actually offsets against the ledger balances, so missing the return deadline means missing the payment deadline.

Monthly filers, meaning businesses with aggregate annual turnover above ₹5 crore or those not opted into the QRMP scheme, file GSTR-3B by the 20th of the following month. January 2026 liability is due by 20 February 2026, February’s by 20 March, and so on. Smaller taxpayers who opt into the Quarterly Return Monthly Payment (QRMP) scheme file quarterly on the 22nd or 24th of the month after the quarter ends, depending on the state of their principal place of business, and still deposit tax for the first two months of each quarter through a PMT-06 challan.⁸

Miss the deadline and two charges apply. Interest runs at up to 18% per annum on the net tax liability that remains unpaid past the due date. From the January 2026 tax period, the portal’s interest calculator factors in any minimum cash balance sitting in your Electronic Cash Ledger between the due date and the actual payment date, which can trim the interest slightly.⁹ Late filing fee runs ₹50 per day (₹25 CGST + ₹25 SGST) for returns with a tax liability, or ₹20 per day (₹10 CGST + ₹10 SGST) for nil returns, capped at ₹10,000 per return.

Interest compounds daily from the day after the due date until the day the tax is actually paid. A business owing ₹2 lakh that files 30 days late pays roughly ₹3,000 in interest alone, with the late fee stacked on top. The portal now auto-populates the interest amount inside GSTR-3B when you open the return.¹⁰

1
CBIC Tax Information. CGST Rules – Rule 87 Electronic Cash Ledger
2
CBIC Tax Information. CGST Act – Section 49 Payment of Tax, Interest, Penalty and Other Amounts
3
GST Portal. List of Authorized Banks for Net Banking and Over the Counter Payments
4
GST Portal. Filing Payment Related Grievances PMT-07
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GST Portal. Filing Form GST PMT-09 for Transfer of Amount
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GST Portal. FAQs – Filing Form GST PMT-09 for Transfer of Amount
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GST Portal. Register and Update DSC
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GST Portal. Form to Change Profile for Quarterly Return and Monthly Payments QRMP Scheme
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CBIC Tax Information. CGST Act – Section 50 Interest on Delayed Payment of Tax
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GST Portal. Advisory on Interest Calculator and Related Enhancements in GSTR-3B