Tax Return Guide for Company Employees
From "Do I even need to file?" all the way to completing the process — explained from scratch.
A clear rundown for employees of the deductions you cannot recover through year-end adjustment, plus the cases that require a tax return — side jobs, medical expenses, mortgage loans and more. It covers everything from the documents you need to how to file with e-Tax.
Year-end adjustment vs. tax return
Which do you need? The difference and how to tell them apart, explained clearly.
BasicsWho needs to file
A decision flow for cases where even employees must file.
CheckDeductions you can recover
Every deduction available only through a tax return, and how much you save.
Tax savingPreparing the documents
What to gather by year-end, as a checklist by situation.
PrepFiling steps (STEP by STEP)
From collecting documents to filing and confirming your refund, step by step.
StepsHow to use e-Tax (e-filing)
The steps for e-filing entirely from your smartphone.
e-TaxFiling for side jobs / miscellaneous income
The ¥200,000 rule, residence-tax cautions, and tips on booking expenses.
Side jobCommon mistakes and fixes
How to handle missed filings, double filing and late submissions.
CautionYear-end adjustment vs. tax return
There are two ways an employee's taxes get settled: year-end adjustment and filing a tax return. Most employees are done with year-end adjustment alone, but depending on the type of deduction or your situation, a tax return may be required — or work in your favor.
- Life insurance premium deduction
- Earthquake insurance premium deduction
- Dependent deduction / spousal deduction
- iDeCo contribution deduction (declared at year-end adjustment)
- Mortgage loan tax credit (second year onward)
- Basic deduction / employment income deduction
- Medical expense deduction
- Furusato Nozei (six or more municipalities / with a side job)
- Mortgage loan tax credit (first year)
- Filing side-job / miscellaneous income
- Offsetting gains and losses on stocks / FX
- Side-job / miscellaneous income over ¥200,000 a year
- Salary over ¥20 million a year
- Receiving salary from two or more places
- First year of the mortgage loan tax credit
- Furusato Nozei (six or more municipalities / with a side job)
- Medical expenses over ¥100,000 (you can get a refund)
- Left a job mid-year (refund of over-withheld tax)
- Losses on stocks / FX (offsetting gains and losses)
- Suffered disaster or theft (casualty loss deduction)
(calculated automatically from income)
(basic, social insurance, life insurance, etc.)
* Year-end adjustment covers the employment income deduction plus the deductions you declared to your employer. A tax return lets you additionally apply deductions such as the medical expense deduction.
Who needs to file a tax return
Even as an employee, a tax return is required — or advantageous — in the cases below. Check whether any apply to you.
Cases where filing is always required
If income other than salary — freelance income, online income, affiliate revenue, stocks, FX and so on — exceeds ¥200,000, you must file. If the "income" after subtracting expenses is ¥200,000 or less, filing is not required.
High earners fall outside year-end adjustment and must file a tax return themselves.
When you receive salary from multiple workplaces, such as a main job plus part-time work. That said, if the side-job salary is ¥200,000 or less a year, filing may not be required.
Rental income, cryptocurrency, lump-sum life insurance payouts, prize winnings and the like. If total income exceeds a set amount, filing is required.
Cases where filing gets tax back (optional, but you should file)
Combine the medical expenses of yourself plus every family member sharing your household. The portion over ¥100,000 becomes eligible for the deduction.
The mortgage loan tax credit requires a tax return only in the first year. From the second year onward it can be completed through year-end adjustment.
If you did not take up new employment after leaving, no year-end adjustment is done, so the tax withheld is often overpaid. You can get a refund by filing a tax return.
The one-stop exception applies only to up to five municipalities. If you are filing together with other deductions such as the medical expense deduction, you must also claim the Furusato Nozei portion on your tax return.
Even with a designated account (with withholding), you must file if you want to carry a loss forward to the next year.
Even when no income-tax return is required (for example, a side job of ¥200,000 or less), there are cases where a residence-tax filing is needed. Residence-tax filings go to your municipality, with a deadline around March 15. If you have side-job income, always check.
List of deductions you can recover
Here are the deductions you can apply only through a tax return, which year-end adjustment does not cover. If any apply to you, simply filing gets tax refunded.
You can file once the whole family's medical expenses exceed ¥100,000 a year. Hospital, dental, medicine and childbirth costs also qualify.
A tax return is required if you donate to six or more municipalities, or file together with other deductions. Do not forget to include the municipalities where you used the one-stop exception.
A tax return is required in the year after you move in. From the second year onward it is completed through your employer's year-end adjustment. Any amount that cannot be fully credited is also deducted from residence tax.
You can offset gains and losses across multiple brokerage accounts. A loss you cannot recover in the current year can be carried forward for three years and offset against future profits (loss carryforward).
If you left a job mid-year and did not receive a year-end adjustment, the amount withheld each month is often too high. Settling it via a tax return gets you a refund.
Applies when your assets are damaged by a typhoon, fire, theft and the like. If the loss is large, it can be carried forward for three years.
Preparing the required documents
The documents a tax return needs vary by situation. Check what to gather for each case.
① Documents everyone needs
It shows salary income, tax withheld, and social insurance premiums. If you have multiple employers, you need one from each. If distributed electronically (PDF), don't forget to download it.
E-filing requires reading the IC chip of your My Number Card. If you have an NFC-capable smartphone, no extra device is needed.
Enter the account for your refund on the return. With e-Tax you can use an account registered in advance.
② Documents needed by type of deduction
- Medical expense receipts (or the "medical expense notice" from your health insurance association)
- Statement of medical expenses for the deduction (created automatically in the Return Preparation Corner)
- Documents showing amounts covered by insurance, etc. (hospitalization benefits, etc.)
- Each municipality's "donation receipt certificate"
- Include receipts from municipalities where you used the one-stop exception
- You can also check via the "donation history" on the portal site
- Calculation statement for the special mortgage loan credit
- Certificate of registered matters (obtained at the Legal Affairs Bureau, around ¥1,000)
- A copy of the real estate sale contract or construction contract
- Year-end mortgage balance certificate (sent by your financial institution)
- Documents showing the home's performance (for energy-efficient / certified housing)
- A summary of income and expenses (accounting software or your own ledger)
- Withholding tax slip (if issued by a client)
- Receipts (evidence for expenses)
- Your brokerage's "annual transaction report" (sent January–February)
- Gather all of them if you have multiple accounts
- Your FX broker's "annual profit-and-loss report"
- Withholding tax slip from the company you left
- Withholding tax slip from your new company (not needed if year-end adjustment was done)
- Unemployment benefits are tax-exempt and need not be filed
Using the "medical expense notice (statement)" sent by your health insurance association saves you the trouble of collecting individual receipts. It also links with Mynaportal, so it can be imported automatically in the Return Preparation Corner.
Filing steps (STEP by STEP)
An employee's tax return goes: collect documents → prepare the return → file → confirm the refund. With e-Tax you can finish in 1–2 hours from home or your smartphone.
Various certificates arrive from year-end through January. The trick is to put them all into a single folder as soon as they arrive.
Your employer issues your withholding tax slip (around January–February). More companies now distribute it electronically (PDF email / web viewing).
Prepare it in the National Tax Agency's "Tax Return Preparation Corner." Just follow the on-screen prompts and the return is completed.
Enter salary income, tax withheld and social insurance premiums. With e-Tax, these can sometimes be imported automatically by linking with Mynaportal.
Enter medical expenses, Furusato Nozei, the mortgage loan, side-job income and so on in order. The screens are in a question-and-answer format, so just answering calculates the deduction amounts automatically.
Once entry is finished, the tax due and refund amount are shown. If the refund is positive, it is worth filing. If negative (extra tax due), pay it by March 15.
There are three ways to file. We recommend e-Tax (smartphone) as the simplest.
- Done entirely with a My Number Card + smartphone
- File anytime, 24 hours a day
- Fast refund (usually within 3 weeks)
- You can skip attaching deduction certificates
- Valid if postmarked by March 15
- Be sure to keep your own copy
- Originals of attachments are required
- Very crowded in February–March
- You can get advice on how to fill it in while filing
- Some Sunday openings (during the filing period)
- With e-Tax, transferred in about 3 weeks after filing
- Paper filing can take 1–2 months
- Enter your account details accurately
- A refund notice is mailed to you first
- Pay by March 15
- Payable by convenience store, credit card or account transfer
- After the deadline, delinquency tax applies
- Direct-debit payment is withdrawn in mid-April
How to use e-Tax (e-filing)
An employee's tax return can be completed with just a smartphone and a My Number Card. Using the Mynaportal app, deduction certificates can be imported automatically too.
Steps to file on your smartphone (My Number Card method)
Works on both iOS and Android. Because it reads your My Number Card via NFC (contactless communication), you need a compatible smartphone (most recent phones support it).
Setting up a link with the "private delivery service" in Mynaportal lets you automatically import deduction certificates from insurers and the pension organization. It is best to finish this setup before the filing period.
Access it from the National Tax Agency site or the "Tax Return" menu in Mynaportal. Select "File on smartphone." As an employee, choose from "Employment income."
Hold the card to the back of your smartphone to read it, and enter the 4-digit PIN (for user certification). If you don't yet have an e-Tax user ID, one is issued automatically at this point.
Enter the withholding tax slip by hand or by camera scan. Linked deduction certificates are entered automatically. Finally press "Submit" to finish. Once a receipt number is issued, filing is complete.
| Filing method | What you need | Refund speed | Difficulty |
|---|---|---|---|
| Smartphone + My Number Card | NFC-capable smartphone, My Number Card | Within 3 weeks | ★★☆ |
| PC + IC card reader | PC, IC card reader, My Number Card | Within 3 weeks | ★★★ |
| ID / password method | ID and password obtained at a tax office (PC) | Within 3 weeks | ★★☆ |
| Paper (mail / counter) | Printing, seal, originals of attachments | 1–2 months | ★☆☆ |
When you link with Mynaportal, the following information is entered automatically on the return (advance setup required).
- Life insurance premium deduction certificate (major insurers)
- National Pension / social insurance premium deduction certificate
- iDeCo contribution payment certificate
- Furusato Nozei donation receipt certificate (some portal sites)
- Year-end mortgage balance certificate (some financial institutions)
- Medical expense notice (from the health insurance association)
Filing for side jobs / miscellaneous income
Employees with side-job income face many tax cautions, and filing incorrectly can cause unexpected trouble. Here are the key points.
Understanding the ¥200,000 rule precisely
over ¥200,000 a year?
An income-tax return is required. Book your expenses properly to save on tax.
However, a residence-tax filing to your municipality is required. Forgetting it can lead to later back-tax charges.
Main expenses you can book for a side job
When you file, setting the residence-tax payment method to "pay it yourself (ordinary collection)" means the residence tax on your side job is paid directly by you rather than from your salary. Because your employer's payroll deduction stays unchanged, this makes it less likely your employer notices the side job. Just choose "pay it yourself" in the "selection of residence-tax collection method" field on the return.
Common mistakes and how to fix them
Here are the failures most common in employees' tax returns. Knowing them in advance prevents most trouble.
If you received a benefit from life insurance while hospitalized, you must subtract that amount from your medical expenses. Forgetting to subtract it overstates the deduction, and a correction may become necessary.
When creating the statement of medical expenses, enter hospitalization benefits and refunds of high-cost medical care in the "amount covered by insurance, etc." field. Verify the amounts against the insurer's payment statement and your health insurance notice.
If you file a tax return after applying for the one-stop exception, the one-stop application is automatically voided. If you then forget to re-declare the Furusato Nozei portion on the return, you lose the deduction.
If you file a tax return, enter all your donations — including the municipalities where you applied for the one-stop exception — on the return. You need to gather donation receipt certificates from every municipality.
When the residence tax on a side job is added to payroll deduction (special collection), the employer's payroll staff may notice.
On page 2 of the return, choose "pay it yourself" (ordinary collection) under the "selection of residence-tax collection method for income other than salary and public pensions." This way the residence tax on your side job is paid by you, with nothing added to your salary.
The mortgage loan tax credit requires a tax return only in the first year, but many people assume "as an employee, year-end adjustment is enough" and forget to file.
Even past the tax-return deadline (March 15), you can file as a "refund return" within 5 years. You can go back five years to recover amounts you had lost, so file as soon as you notice.
An error in the account number, or specifying an old account, means the refund is not deposited and the process becomes complicated.
Always check the account details (financial institution name, branch name, account number) before submitting the return. If you made a mistake, contact the tax office to make a correction. With e-Tax you can check via the preview before submitting.
For a refund return there is no penalty for missing the deadline since you can file anytime within 5 years, but if extra tax is due, delinquency tax and a failure-to-file penalty apply.
If it is a refund only, you can file as a "refund return" within 5 years even after the deadline. If extra tax is due, filing voluntarily before the tax office points it out reduces the penalty tax to 5% (the minimum).
• Deduction certificates arrive from insurers
• Mortgage balance certificate arrives
• Submit year-end adjustment forms to your employer
• Year-end adjustment (done by your employer)
• Over/underpayment settled in the December salary
• Final check of medical receipts / Furusato Nozei receipts
• Furusato Nozei receipts arrive (some)
• Annual stock transaction reports arrive
• Withholding tax slips are issued
• From 2/16: tax-return filing opens
• Prepare and submit the return via e-Tax
• Refund returns are possible from January 1
• 3/15: tax-return and payment deadline
• If extra tax is due, pay within the deadline
• With an e-Tax filing, refund in about 3 weeks
• Residence-tax decision notice arrives (June)
• Check the Furusato Nozei residence-tax deduction (June)
Explore related columns in more depth
How to calculate the medical expense deduction
What qualifies, the calculation, netting reimbursements, and self-medication.
Furusato Nozei guide
The deduction breakdown, the cap, the one-stop exception and the 2025 revisions.
Filing for side jobs
The precise meaning of the ¥200,000 rule and the residence-tax pitfall.
Risks of a pair loan
Sharing the mortgage loan tax credit between two people — group credit life insurance, divorce and ownership-share cautions.
FAQ
Does anything get relayed to my employer if I, as an employee, file a tax return?
For refund returns only, such as the medical expense deduction or Furusato Nozei, no notice is generally sent to your employer. If you have side-job income, choosing "pay it yourself" as the residence-tax collection method makes it less likely the side-job residence tax is added to your payroll deduction (if the side job is salary, it may not be separable).
Can I claim a deduction later if I forgot to file it?
Refund returns such as the medical expense deduction or the first year of the mortgage loan tax credit can be filed retroactively within 5 years from January 1 of the year following that year.
Which is better, e-Tax or paper filing?
With e-Tax, if you have a My Number Card you can file from a smartphone or PC, skip some attachments, and get your refund faster. The filing deadline is generally March 15.
Sources / official information
This article is based on the official information below. Rules may be revised. Please check each official site for the latest details.
- National Tax Agency, Tax Answer No.1900 — Salary earners who must file a tax return (in Japanese)
- National Tax Agency — Tax Return Preparation Corner (in Japanese)
- e-Tax (National Tax Electronic Filing and Payment System) (in Japanese)
- National Tax Agency, Tax Answer (common tax questions) (in Japanese)
* This article is for informational purposes only and is not tax or legal advice. For individual tax judgments, consult your local tax office or a licensed tax accountant (zeirishi).