Year-End Adjustment or Tax Return? Which One Applies

Quick Answer: These are not two options you choose between. 年末調整 is something your employer does to you in December. 確定申告 is something you file yourself, and it splits into two very different cases: filings you are legally required to make, and filings you are merely allowed to make — the second of which can go five years back.

Every autumn the same question circulates in foreign-resident groups in Japan: do I do 年末調整 or 確定申告?

It is the wrong question, and it produces the wrong answer. For most salaried employees the year-end adjustment is not a choice at all — it happens whether you engage with it or not. The real decision sits somewhere else entirely, and a lot of people never find it.

This is educational information, not tax advice. Your obligations depend on your income, employment and circumstances — confirm with the NTA or a qualified tax professional (税理士).

What does 年末調整 actually do?

Your employer withholds income tax from every payslip, but that withholding is an estimate based on your expected annual income. By December it needs reconciling against what you actually earned and what deductions you actually qualify for.

That reconciliation is the year-end adjustment. You hand in a couple of forms in November, your employer recalculates, and the difference shows up in your final pay of the year — usually as a refund.

For most employees, that is the entire tax year. No return, no tax office, nothing else required. Which is exactly why so many people never learn what it does not cover. The deductions it handles and the ones it doesn't are set out in your first Japanese payslip, decoded.

Who is actually required to file a return?

This part is not a judgement call — the NTA lists the categories. A salaried employee must file if any of these apply:

If none of those describe you, you are not required to file. Most foreign employees on a single salary are in that group.

And that is where the interesting part starts, because "not required" is not the same as "no reason to."

What can the year-end adjustment never handle?

Some deductions are simply outside its scope. Your employer cannot apply them no matter how helpfully they fill in your forms. The common ones:

If any of those apply and you do nothing, nobody chases you. The money simply stays with the tax office. That is the actual cost of treating this as a binary choice — you never file, so you never claim.

What if you're not required to file, but should?

This is the part worth knowing, and it is the reason the deadline panic is mostly misplaced.

A filing made purely to reclaim over-withheld tax is a 還付申告 — a refund return. It is not bound by the 16 February to 15 March window, and the NTA is explicit about how long you have:

「その年の翌年1月1日から5年間提出することができます。」

Five years, starting from 1 January of the following year.

So if you paid for a major medical year in 2022 and never claimed it, that claim is very likely still open. Same for a Furusato year where you went over five municipalities and forgot to file. You are not late. You have simply not got round to it yet.

Two practical notes: this applies to refunds, not to filings you were required to make — if you had to file and didn't, that is a different and more urgent conversation. And some specific benefits do require filing by the statutory deadline even when a refund is involved, so a large or unusual claim is worth checking rather than assuming.

What does the calendar actually look like?

When What
November Your employer hands you the year-end adjustment forms
December The adjustment runs; the difference appears in your final pay
16 Feb – 15 Mar The 確定申告 window, for anyone required to file
Any time, 5 years 還付申告, for anyone filing only to claim a refund
June Resident tax for the year catches up, based on all of the above

To see how the withholding this all reconciles against is calculated in the first place, the Japan Tax Calculator estimates it from your gross salary.

Frequently Asked Questions

Do I need to file a tax return in Japan if I'm a salaried employee?

Usually not. If you have one employer, salary under ¥20 million, and less than ¥200,000 of other income, your year-end adjustment settles your income tax and no return is required. You may still choose to file to claim deductions your employer cannot apply.

What is the ¥200,000 rule?

If you have one employer and your other income — side work, rental, certain investment income — exceeds ¥200,000 in the year, you are required to file a return. With two or more employers, the test combines un-adjusted salary with that other income against the same ¥200,000 threshold.

Can I claim a Japanese tax refund for previous years?

Generally yes. A return filed purely to claim a refund can be submitted for five years from 1 January of the year after the tax year in question, and is not restricted to the February–March window. Missed medical expense claims are the most common example.

What can't the year-end adjustment do?

It cannot apply the medical expense deduction, Furusato Nozei where you used six or more municipalities, the housing loan credit in its first year, or donations to other qualifying bodies. Those require a return regardless of whether you are otherwise obliged to file one.

Does 年末調整 happen automatically?

Effectively, yes — but it depends on you returning the forms your employer gives you in November, with the dependants and insurance details filled in. An unreturned form means deductions you are entitled to simply don't get applied.

PlanTogetherFI is for educational planning only. It is not tax, financial or legal advice. Filing obligations depend on your income, employment situation, residency status and circumstances, and thresholds can change — confirm your own position with the NTA or a qualified tax professional (税理士).

Sources and further reading

Rules reflect the position as of September 2026 and can change. Confirm your own obligations with the NTA.