Paying your Corporation Tax after you file

Short version. Once HMRC accepts your CT600, the amount you owe usually appears in your company’s HMRC account within a few working days. You don’t have to wait for it to show up to pay. Corporation Tax is self-assessed, so you can pay as soon as you know the figure (your filing receipt shows it). Pay HMRC directly using the 17-character payment reference for that accounting period, and note that reference is different every year, so don’t reuse last year’s. Payment is due 9 months and 1 day after your accounting period ends.

1. When your Corporation Tax shows in your HMRC account

When you file a CT600, you’re telling HMRC how much Corporation Tax your company owes. You work it out, not HMRC (this is called self-assessment). After HMRC accepts the return, that figure is posted to your company’s Business Tax Account, under “View your Corporation Tax”.

In practice the amount usually appears within a few working days of acceptance, often within a day or two, sometimes the same day, and occasionally longer at busy times. HMRC doesn’t publish a guaranteed timescale for this, so treat “a few working days” as the expectation rather than a promise. Your acceptance/receipt from SimpleCompanyTax (with the IRmark) is your proof the return reached HMRC, and it already shows the tax figure.

2. Can I pay before it shows in the account?

Yes, and you often should. Because Corporation Tax is self-assessed, you don’t need to wait for the figure to appear online before paying. As long as you use the correct payment reference for the accounting period (see below), HMRC will match your payment to the right period when the return is processed.

This matters because the deadline to pay is earlier than the deadline to file(section 6), so many companies pay before they file (or at the same time), rather than waiting for the portal to update.

3. How to pay HMRC

You pay HMRC directly. SimpleCompanyTax files your return but does not collect or pass on the Corporation Tax itself. The official options are on gov.uk’s “Pay your Corporation Tax bill” page. The common ones, fastest first:

• Online or telephone bank transfer: Faster Payments usually reaches HMRC the same or next day, CHAPS the same working day, and Bacs takes around 3 working days.
• Debit card or corporate credit card online (personal credit cards aren’t accepted, and a corporate card may carry a fee).
• Direct Debit through your HMRC online account: allow about 5 working days the first time you set one up, fewer once it’s in place.

Allow enough time for the payment to clear by the deadline, because it’s the date the money reaches HMRC that counts, not the date you send it. If no tax is due (for example a loss or a dormant period), you tell HMRC there’s “nothing to pay” rather than making a payment.

4. Your payment reference, and why it changes each year

Every Corporation Tax payment needs a 17-character payment reference. It is built from your company’s fixed 10-digit Unique Taxpayer Reference (UTR) plus a short suffix that identifies the specific accounting period you’re paying, for example 1234567890A00108A.

The important part: the suffix changes for every accounting period. Your UTR stays the same year after year, but the full 17-character reference is different each year. Don’t reuse last year’s reference. If you do, HMRC may credit the payment to the wrong year, which can leave the current year looking unpaid (and the wrong year in credit).

You’ll find the correct reference on HMRC’s payment reminder or payslip, and in your HMRC online account when you choose to pay a particular period.

5. Do I need to choose the accounting period before paying?

Effectively, yes, and you do it through the reference. There isn’t a separate “which year?” question to answer. The 17-character reference is how HMRC knows which accounting period your money belongs to. Pick the reference for the period you’re paying (in the online account you select the period, which gives you its reference), and the payment lands against that period.

This is the single most common mistake: paying the right amount with the wrong period’s reference. Get the reference right and the period takes care of itself.

6. Payment deadline vs filing deadline

These are two different dates, and the payment one usually comes first:

• Pay your Corporation Tax: by 9 months and 1 day after the end of your accounting period.
• File your CT600: by 12 months after the end of your accounting period.

So for most companies the tax is due to be paid before the return is due to be filed. That’s exactly why paying before the portal updates is normal, and why it’s worth filing in good time so you know the precise figure ahead of the payment date.

7. What most companies do

In our experience, the typical, low-stress approach is:

• File first to lock in the exact figure (your SimpleCompanyTax receipt shows the tax due).
• Pay HMRC directly soon after (most by Faster Payments bank transfer because it’s quick and free), using that period’s 17-character reference.
• Don’t wait for the amount to appear in the HMRC account. Pay by the 9-months-and-1-day deadline and let the online balance catch up.

This is general guidance for a straightforward UK micro-entity, not advice about your specific company. For the authoritative detail (current methods, processing times and your exact figures), use gov.uk “Pay your Corporation Tax bill” and your HMRC Business Tax Account.

Related: What is a CT600? · How to file company tax