Year-End Adjustment vs. Final Tax Return: What Expats Working in Japan Need to Know

A must-read for expats working in Japan: understand the difference between the year-end adjustment (年末調整) and the final tax return (確定申告) — when you must file yourself, how to file online via e-Tax, the March 15 deadline, and the most common refund scenarios.

The Key Difference Between the Two

Item	Year-End Adjustment (年末調整)	Final Tax Return (確定申告)
Who files	Employer files on the employee's behalf	You file directly with the tax office
Who it's for	Salaried employees (給与所得者)	Freelancers, multi-income earners, certain salaried employees
Period	November–December (handled internally by employer)	February 16 – March 15 each year
How to file	Fill in forms provided by employer	Complete the tax return (paper or e-Tax online)
Visit tax office?	Usually not required	Usually completable online (e-Tax)

In short: Year-end adjustment = your employer handles it. Final tax return (確定申告) = you handle it yourself.

When Do You Need to File a Final Tax Return (確定申告) Yourself?

Even if your employer completed the year-end adjustment, you still need to file a final tax return (確定申告) in the following situations:

Scenarios Requiring a Final Tax Return (確定申告)

Freelance or side income exceeding ¥200,000
- Examples: Uber Eats delivery, freelance contracts, YouTube ad revenue
Working multiple jobs simultaneously
- Income from employers other than your primary employer is usually not covered by year-end adjustment
Annual income exceeds ¥20,000,000
Left a job mid-year without finding new employment
- Year-end adjustment can only be done by an employer you have at the end of the year — if you're unemployed at year-end, you must file yourself
Rental income from property
Capital gains from stocks or investment funds (outside of a specific account (特定口座))
Applying for the housing loan deduction (住宅ローン控除) in the first year
hometown tax donation (ふるさと納税) beyond the limit manageable by one-stop exemption (ワンストップ特例)
Medical expenses exceeding ¥100,000 (医療費控除)

📌 Working holiday participants: If you changed jobs mid-year or were unemployed at year-end, you typically need to file a final tax return (確定申告). Make sure to keep the withholding certificate (源泉徴収票) from every employer — you'll need them when filing.

How to File a Final Tax Return (確定申告): Step by Step

Step 1 — Gather Required Documents

Document	Notes
Withholding certificate (源泉徴収票)	Issued by each employer, usually in January
My Number card or notification card	For identification on the return and e-Tax authentication
Deduction certificates	Life insurance, iDeCo contribution certificates, etc. (mailed November–December)
Bank account details	For receiving any refund

Step 2 — Complete the Return Online (e-Tax Recommended)

Go to the National Tax Agency's online filing portal
Select start creation (作成開始) → income tax (所得税)
Follow the prompts, entering each income source and deduction
The system automatically calculates your tax owed or refund amount
Sign electronically using your My Number card and submit (e-Tax method)

💡 First time using e-Tax? Prepare your My Number card in advance, along with the card reader PIN (4 digits) and electronic signature password (6–16 characters). If you've forgotten your passwords, reset them at your local city hall.

Step 3 — Pay Tax Due or Wait for Refund

Tax due: The return will show a tax payable (納付税額). Pay via convenience store, PayPay, or bank transfer
Refund: If more was withheld during the year than you owe, filing a final tax return (確定申告) typically yields a refund — deposited to your designated bank account within 3–6 weeks

Common Deductions You Can Claim

Deduction	Description
Medical expense deduction (医療費控除)	Medical expenses (for you and your family) exceeding ¥100,000/year
Hometown tax donation (ふるさと納税)	Hometown tax donations to local governments — major tax credit
Life insurance premium deduction (生命保険料控除)	Life insurance and medical insurance premiums
iDeCo (individual defined contribution pension)	Full monthly contribution amount is deductible
Donation deduction (寄附金控除)	Donations to certified NPOs and other organizations

Residents vs. Non-Residents: How It Affects Expats

Japan's tax law distinguishes between "residents" and "non-residents":

Resident (居住者): Lives in Japan for more than 1 year, or has their primary base of life in Japan within a 12-month period → Must report worldwide income to Japan
Non-resident (非居住者): Stays in Japan for less than 1 year without establishing a life base → Only reports Japan-source income

Most expats working in Japan on work or student visas for more than a year are classified as residents and follow resident rules.