GuidesPublished 2026-05-20Updated 2026-11-1010 min read

Final Tax Return: Who Files, When, e-Tax / Refund / Tax Manager

Employees with year-end adjustment usually don't file. Over ¥20 million in salary or over ¥200,000 of other income means you must file; ¥100,000+ medical expenses, 6+ Furusato Nozei donations, or a mid-year resignation are reasons to file for a refund. New e-Tax users need a My Number card, paper postmark = filing day, refund typically arrives 3-6 weeks.

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Final Tax Return (kakutei shinkoku) recalculates January 1 to December 31 income, deductions, and prior tax withholdings, and reports them to the local tax office. Income tax filing is usually from February 16 to March 15 of the following year (postponed for weekends/holidays; check the National Tax Agency for the year’s official announcement). Company employees with one salary source are usually handled by year-end adjustment and don’t need to file. Side income, medical expenses, Furusato Nozei (hometown tax donation), mid-year resignation, or leaving Japan each need a check against the NTA conditions, and some of them are optional refund claims rather than duties. This article splits it into 5 stages: judging → documents → submission → resignation/move/return-home → preservation, with concrete deadlines and amounts.

1. Start with the source-deduction certificate

The Source-Deduction Certificate (gensen-choshu-hyo) is the most basic document. It lists payment amount, post-deduction salary, deduction total, withholding tax, and company name. December-active employees are usually issued post-year-end-adjustment; mid-year resignees should request it from the prior company too (per Income Tax Act Article 226, issuance within 1 month of resignation is the company’s duty).

After receiving, verify: name, address, My Number submission status, dependent count, insurance deductions. Address errors propagate through tax office → residence tax notice → municipal records; people who resigned and moved in 2026 especially need to confirm the prior company’s mailing address.

Cases needing 2+ certificates: mid-year job change (prior + current employer), side income from a second salary source, post-resignation re-employment. All certificates must be summed for joint income calculation.

Sources: NTA No.7411: Issuance of Source-Deduction Certificate, Income Tax Act Article 226.

2. When you must file, and when filing gets money back

Two different questions get mixed up here: whether the law requires you to file, and whether filing is worth it because it returns tax. For a company employee, the main cases split like this.

Filing is required:

Case	Criterion	Notes
Salary income exceeds ¥20,000,000	Year-end adjustment does not cover it	Regardless of industry
Other income exceeds ¥200,000	Income (revenue minus expenses) other than salary and retirement pay, such as writing fees, contract work, freelance, crypto gains, real estate	Stock gains in a withholding tax-designated account (tokutei koza, gensen ari), if you choose not to declare them, and NISA gains do not count toward the ¥200,000
Two+ salary sources and the non-adjusted salary exceeds ¥200,000	Including side jobs, temporary salary

Filing is optional but returns tax (refund claim, kanpu shinkoku):

Case	Criterion	Notes
Resigned mid-year, didn’t re-employ within the year	Year-end adjustment not done	Withholding is usually too high, so filing usually yields a refund
Medical expense deduction	Annual paid medical expenses exceed ¥100,000 (or 5% of income if total income is under ¥2,000,000)	Family aggregate possible
Furusato Nozei to 6+ municipalities	One-Stop Special doesn’t apply	Without filing, the donation deduction is not given

The ¥200,000 rule is a filing exception, not a tax exemption. If you file for any other reason, such as a medical expense refund, the side income must be included in that return too. Residence tax has no ¥200,000 exception, so declare it to the municipality.

Medical expense deduction calculation: deduction = paid medical expenses − insurance reimbursements − ¥100,000 (or 5% of income if total income is under ¥2,000,000). Cosmetic, preventive, and ordinary supplements are excluded, but prescription medications, hospitals / pharmacies / dentistry / vision correction, fertility treatment, and outpatient travel (public transit only) are covered.

The One-Stop Special (Furusato Nozei without final filing) has conditions: ≤5 donation municipalities + no final tax return filed for that year. 6+ municipalities, or filing a return for any reason, means the donations have to be included in the final return.

Sources: NTA No.1900: Salary Earners Required to File, NTA No.1120: When You Pay Medical Expenses, NTA: For those who made Furusato Nozei donations.

3. Documents and filing: e-Tax / paper / refund

Basic documents: source-deduction certificate, identity verification (My Number card or My Number notice + driver’s license), bank account (for refund deposit), deduction certificates (insurance, donations, medical bills), donation receipts (Furusato Nozei), residence card (foreigners).

Three submission methods:

Method	Operation	Suits
e-Tax + My Number card	Smartphone NFC read, 30-60 min	My Number card + 4-digit PIN holder, fastest
e-Tax + ID/Password method	New IDs and passwords stopped being issued on October 1, 2025	Only people who already have them
Paper (mail / window)	Print at Final Tax Return Form Preparation Corner, postmark = filing day	Those without a My Number card, or uncomfortable with online

The ID/password method was a stopgap until My Number cards spread. If you never got credentials, use the My Number card method or file on paper.

e-Tax advantages: refunds typically arrive within 3 weeks (paper takes 4-6 weeks), deduction certificate attachment omitted, automated calculation. My Number card smartphone filing is the dominant method since 2024.

Payment methods (when tax is owed): direct deposit (account debit, late April lump sum), QR code (convenience store payment, ≤¥300,000), online banking, credit card, tax office window. Credit card payment adds a processing fee of ¥99 for each ¥10,000 of tax (¥99 up to ¥10,000, ¥198 up to ¥20,000, and so on); the payment site shows the exact amount. Direct deposit is most convenient; just tick at filing.

Late payment and late filing: late payment interest (entaizei) is reset every year. For 2026 it is 2.8% a year for the first 2 months after the due date and 9.1% after that (2025: 2.4% and 8.7%); 7.3% and 14.6% are only the statutory caps. Not filing on time adds a no-filing penalty: 15% to 30% if you file after a tax audit (30% on the portion over ¥3,000,000), reduced to 5% if you file on your own before the tax office contacts you.

Sources: NTA: Final Tax Return Form Preparation Corner, NTA: e-Tax online filing system, NTA: stop of new ID/password issuance (2025), NTA: credit card payment Q&A, NTA No.9205: Late Tax.

4. Mid-year resignation / moving / return-home: 3 special cases

Mid-year resignation without re-employment: Year-end adjustment not done by the company, withholding tax has typically been over-withheld; filing usually yields a refund. Calculation: annual salary minus the salary income deduction, the basic deduction, and other deductions (social insurance, life insurance, etc.) → correct income tax → the difference from withholding tax is the refund. The basic deduction depends on the year and your total income. For 2026 income it is ¥1,040,000 if total income is ¥4.89 million or less, ¥670,000 up to ¥6.55 million, and ¥620,000 up to ¥23.5 million; for 2025 income it was ¥580,000 to ¥950,000. Old guides that use ¥480,000 underestimate the refund.

Moving: Filing location is judged by “address at time of filing.” Prior employer / municipality may send notices to the prior address; confirm postal forwarding (max 1 year free) is set up.

Pre-departure settlement (leaving Japan permanently) follows 3 steps. First, if anything for national tax will arrive after you leave, file a Tax Manager Notification with the tax office, choosing a representative from family, a tax accountant, or a friend. Second, settle residence tax with the municipality, which is a separate procedure. Residence tax is charged in full to whoever lived in the municipality on January 1, based on the previous year’s income; leaving mid-year does not reduce it. Pay the remaining installments before you go, or register a local tax representative with the ward or city office. If you leave between January 2 and about June, the next fiscal year’s tax will still be assessed, so you need that representative even after the current year is paid. Third, request the pension lump-sum withdrawal: foreigners with 6+ months of contributions can apply within 2 years of the day they no longer have an address in Japan, and 2 years is a hard deadline. Starting these 3 steps 3 months pre-departure is the safe plan.

Sources: NTA No.1923: Overseas Assignment and Tax Manager, NTA No.1199: Basic Deduction, Itabashi City: resident tax procedures when moving abroad, Koto City: resident tax tax representative when leaving Japan, JPS: Lump-Sum Withdrawal Request.

5. How long to keep records and where to ask

Filing copies, e-Tax receipt notices, payment receipts, refund notices, source-deduction certificates, medical receipts, and donation receipts should be kept by year. Legal requirement: blue-return filers 7 years, white-return filers 5 years. Company employees’ source-deduction certificates have no strict obligation, but next visa renewal, loan, rental, nursery application, and income proof commonly request 1-3 years of tax records. 5 years is a safe baseline.

Where to consult when uncertain: NTA web judgment flow has case-by-case judgment; phone consultation center (0570-00-5901, weekdays 8:30-17:00); nationwide 524 tax office windows (during 2-3 March filing period, reservation priority); tax accountants (individual cases ¥30,000-100,000, complex cases ¥100,000-300,000). “This is exempt” claims on social media are meaningless; tax decisions depend on the combination of income type, amount, residency status, withholding tax, and deduction items.

Sources: NTA: No.2080 bookkeeping and record keeping for white-form filers, NTA: Tax Consultation Service, 国税庁の概要.

6. Common mistakes

Assuming side income of ¥200,000 or less is tax-free. It only means you may not need to file an income tax return for it. If you file anyway (for a medical refund, for example), it must be included, and residence tax has no ¥200,000 exception, so declare it at the municipal office. Missing it can result in back-charging and potential underreporting.

Calculating medical expense deduction per individual. Correct approach is family aggregation (same household, including non-co-resident dependent children). The ¥100,000 annual threshold is per-aggregation; per-individual calculation may miss it.

Using the One-Stop Special for all donations within 5 municipalities. If you file a return for any reason (medical expenses, etc.), the One-Stop application no longer counts, and the donations must also be in the final return. Otherwise the donation deduction is not given.

Not receiving the source-deduction certificate after resignation. Income Tax Act Article 226 requires issuance within 1 month of resignation. If it does not come, ask the prior employer again and keep a note of when and how you asked. If they still do not issue it, submit a Notification of Non-Issuance of a Withholding Certificate to the tax office, which will then ask the employer to issue it. The refund is not lost because the paper is late.

Pre-departure only designating a Tax Manager for national tax, ignoring residence tax. Residence tax is a separate local procedure, assessed in full for the year on your January 1 address and not reduced for the months you are abroad. Pay it off or register a representative with the municipality. Non-payment incurs late charges and can show up later on a tax certificate (nozei shomeisho) when you need one for a visa.

Believing all the “this is exempt” claims on social media. Each person’s combination of income type, amount, residency status, withholding tax, and deductions differs; NTA web judgment, tax accountant, or tax office confirmation is the safe approach.

Sources: NTA No.1900: Salary Earners Required to File, NTA F5-4: Notification of Non-Issuance of Withholding Certificate.

Japanese key terms

確定申告 (kakutei shinkoku, Final Tax Return)
還付申告 (kanpu shinkoku, refund claim)
源泉徴収票 (gensen-choshu-hyo, Source-Deduction Certificate)
年末調整 (nenmatsu-chosei, year-end adjustment)
医療費控除 / ふるさと納税ワンストップ特例 (Medical Expense Deduction / Furusato Nozei One-Stop Special)
e-Tax / マイナポータル連携
納税管理人 (nozei-kanrijin, Tax Manager)