Self Assessment Late Filing and Payment Penalties

The Self Assessment year runs to 5 April, and two filing deadlines follow: 31 October for paper returns and 31 January for online returns (the same 31 January by which any balancing payment and first payment on account are due). Miss the deadline that applies to you and the penalty regime in Schedule 55 of the Finance Act 2009 engages automatically — there is no discretion and no warning letter first.

Three points catch people out:

• Penalties do not depend on owing tax. The fixed and daily penalties are charged even where your liability is nil or HMRC owes you a refund. Only the 6- and 12-month tax-geared penalties scale with the tax due (subject to the £300 minimum).
• A Notice to File creates the obligation. If HMRC has issued you a notice to file, you must file — even if you believe you have no tax to pay. If you think you no longer need to be in Self Assessment, ask HMRC to withdraw the notice before the deadline rather than ignoring it.
• Paper filers get the earlier deadline. File a paper return in December and you are already two months late, even though the online window is still open. Filing online after missing the paper deadline resets you to the 31 January test.

The filing penalties stack in four stages, each measured from the filing deadline:

• 1 day late: fixed £100 penalty, immediately.
• 3 months late: daily penalties of £10 per day for up to 90 days — a maximum of £900.
• 6 months late: a further penalty of 5% of the tax due or £300, whichever is greater.
• 12 months late: another 5% or £300, whichever is greater. Where HMRC decides you deliberately withheld information by not filing, this final penalty can rise to 70% or 100% of the tax due (concealment cases).

So a return filed just over a year late costs at least £1,600 in filing penalties alone (£100 + £900 + £300 + £300), before any late payment charges or interest. For higher liabilities the 5% figures overtake the £300 minimums and the totals climb steeply.

Partnership returns are harsher still: the fixed penalties are charged on every partner individually, and only the nominated partner can appeal on behalf of all of them.

Our Self Assessment late filing penalty calculator maps every trigger date for your tax year and estimates the penalties for your expected filing date.

Paying late is penalised separately from filing late — you can file on time and still collect payment penalties, or file late having paid on time and avoid them entirely. Under Schedule 56 Finance Act 2009, the charges on unpaid Self Assessment tax are:

• 30 days late: 5% of the tax unpaid at that date.
• 6 months late: a further 5% of what is still unpaid.
• 12 months late: a further 5% of what is still unpaid.

On top of the penalties, late payment interest runs daily from the day after the due date until payment. Since 6 April 2025 the rate is set at the Bank of England base rate plus 4 percentage points — 7.75% from 9 January 2026. Interest is charged on the penalties too once they fall due, and there is no appeal against interest itself (only against the penalties).

One nuance worth knowing: the 5% late payment penalties apply to the balancing payment, not to payments on account. Miss a 31 July payment on account and you accrue interest, but not a 5% penalty. The penalty regime bites at the following 31 January when the balancing payment falls due.

If you cannot pay, the single most valuable move is to set up a Time to Pay arrangement before the next penalty trigger date. Where an arrangement is in place and you keep to it, the 5% late payment penalties that would otherwise be charged during the arrangement are not applied. Interest continues to run — Time to Pay spreads the debt, it does not discount it.

For Self Assessment debts of £30,000 or less, HMRC's online payment plan service usually lets you set up instalments yourself within 60 days of the payment deadline, without speaking to anyone — you need your return filed and no other HMRC payment plans or debts. Larger debts, older debts, or other taxes mean a call to HMRC's Payment Support Service to negotiate a bespoke arrangement based on your income and outgoings.

Two cautions. First, Time to Pay does nothing for filing penalties — file the return even if you cannot pay a penny, because filing stops the worst of the ladder and lets HMRC calculate the real debt. Second, defaulting on an arrangement revives HMRC's full collection powers, and a broken plan is much harder to replace. See our separate guide to Time to Pay arrangements with HMRC for the negotiation detail.

You can appeal any late filing or late payment penalty within 30 days of the date on the penalty notice — online through your HMRC account, or by post on form SA370 (SA371 for partnership penalties). Late appeals need a reason for the delay as well.

The main ground is reasonable excuse: something unexpected or outside your control that prevented you meeting the deadline, provided you then filed or paid without unreasonable delay once the obstacle passed. HMRC's published examples include:

• the death of a partner or close relative shortly before the deadline;
• an unexpected hospital stay, or a serious or life-threatening illness;
• a computer or software failure while preparing your online return, or problems with HMRC's online services;
• fire, flood, or theft; unpredictable postal delays; or delays related to a disability or mental illness.

What does not count: relying on insufficient funds (unless caused by events outside your control), finding HMRC's online system too difficult, not receiving a reminder, or making a mistake on the return. Reliance on an accountant who failed to file is normally not enough on its own — though HMRC also has a discretionary power to reduce a penalty in "special circumstances", which is worth raising in genuinely unusual cases.

Always file before (or with) the appeal. An outstanding return undermines almost any excuse, and the daily penalties keep accruing while you argue. If HMRC rejects the appeal you can ask for a statutory review or take the case to the First-tier Tax Tribunal.

Suppose your 2025/26 return (online deadline 31 January 2027) is filed on 15 December 2027 — about ten and a half months late — with £5,000 of tax due, all still unpaid:

• Filing penalties: £100 fixed + £900 daily (the full 90 days from 1 May 2027) + £300 at the 6-month point (greater of £300 or 5% of £5,000 = £250). Total: £1,300. Filing before 31 January 2028 avoids the 12-month charge.
• Payment penalties: 5% at 30 days (£250) + 5% at 6 months (£250). Total: £500.
• Interest: daily on the £5,000 (and later on the penalties) at base rate + 4% for the whole period.

The same return filed one day late with the tax paid on time would have cost £100. The lesson is mechanical: every trigger date you get ahead of — by filing, paying, or agreeing Time to Pay — removes a whole rung of the ladder. Run your own dates through the penalty calculator to see which rungs you can still avoid.