freee HR : 2024 Year-End Tax Adjustment Guide for Employees (English Ver. )
freee K.K
Disclaimer: This is a provisional translation, and therefore, no responsibility or liability will be assumed for its accuracy, completeness, or use. The original document in Japanese should be referred to for any authoritative interpretation or legal reliance.
Understanding Japan’s Year-End Tax Adjustments
( 年末調整 - Nenmatsu Chosei)
Withholding Tax
Year-End Tax Adjustment
In Japan, employers are required to withhold income tax from their employees' salaries each month and remit it to the government, a process known as withholding tax or 源泉徴収 (Gensen Choshu). The income tax is calculated based on the employee's salary and is automatically deducted at the time of payment. This system relieves employees from the responsibility of directly paying the tax, as employers handle both the deduction and payment on their behalf.
At the end of each year, employers must calculate whether the taxes withheld from an employee's monthly salary accurately reflect their total annual income. This process is called year-end tax adjustment or 年末調整 (Nenmatsu Chosei).
If an employee's annual salary is less than 20 million yen, they are subject to this year-end tax adjustment. For employees earning over 20 million yen, they must file their own tax return or 確定申告(Kakutei Shinkoku). During this adjustment, employees can claim several deductions that were not considered in the monthly withholding, and their total annual tax liability is recalculated based on these deductions. Any discrepancies between the annual tax owed and the amount already withheld are adjusted, and the difference is typically refunded through the employee’s payroll, usually in December or January of the following year.
This system allows employees whose sole income is their salary to have their taxes automatically adjusted, avoiding the need to file a tax return. However, a tax return is required in certain situations, such as when an employee has income from a second job.
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Deductions Available for Year-End Tax Adjustments
Japanese | Hiragana | English Translation | Description |
基礎控除 Kiso Kojo | きそこうじょ | Basic Deduction | Applicable according to the amount of income
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配偶者控除 Haigusha Kojo | はいぐうしゃこうじょ | Spouse Deduction | Applicable, if the total amount of income is 10,000,000 yen or less, with a spouse whose income is 480,000 yen or less
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配偶者特別控除 Haigusha Tokubetsu Kojo | はいぐうしゃとくべつこうじょ | Spouse Special Deduction | Applicable, if the total amount of income is 10,000,000 yen or less, with a spouse whose taxable income between 480,001 yen and 1,330,000 yen
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扶養控除 Fuyo Kojo | ふようこうじょ | Dependent Deduction | Applicable for dependents having total amount of income 480,000 yen or less among relatives who is 16 years old or older, living in the same household with you.
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保険に関する控除 Hoken ni Kansuru Kojo | ほけんにかんするこうじょ | Insurance-related Deduction | Applicable for Life Insurance Premium, Earthquake Insurance Premium, Social Insurance Premium, Small Business Mutual Aid Premium
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In addition, there are various types of deductions, such as the home loan deduction (住宅ローン控除), the widow/widower or single parent deduction (寡婦/ひとり親控除), the disability deduction (障害者控除), the working student deduction (勤労学生控除), and the income adjustment deduction (所得調整控除). Please refer to the National Tax Agency website for details. | |||
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Key Considerations for Year-End Tax Adjustments
Eligibility for Year-End Adjustment
Dependent Family Members
“Those who have a dependent relative who is 16 years old or older; only those having total amount of income 480,000 yen or less among relatives who is 16 years old or older, living in the same household with you (including a foster child and the elderly, but excluding your suppose, a person who receive salary payment as a family employee of blue return taxpayer, or a family employee of white return taxpayer. The same applies hereinafter.”
In Japan, most employees are subject to year-end adjustment. Those who are not subject to year-end adjustment are as follows:
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Once you receive an input request by e-mail or LINE, access freee HR from the URL provided and start your year-end adjustment process. You can also access the system from your smartphone as well as from your PC.
*For users who are utilizing a login ID that does not use an email address, email notifications will not be sent. Therefore, when you receive guidance from your HR representative, please log in to freee HR and proceed with the “year-end adjustment.”
Access the Year-End Adjustment System in freee HR
Please be aware that there is a deadline for submitting year-end adjustments.
Make sure to submit your application well ahead of time!
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The screenshots in this manual are taken from Chrome’s automatic translation extension. Please note that automatic translation is an assistive tool, and freee is not liable for any damages, including but not limited to mistranslations, that may occur from using this feature.
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How to Complete the Year-End Adjustment in freee HR
There are five items that you will need to confirm.
（Please refer to the help pages for each item here.)
Please note the following:
The screenshots in this manual are taken from Chrome’s automatic translation extension. Please note that automatic translation is an assistive tool, and freee is not liable for any damages, including but not limited to mistranslations, that may occur from using this feature.
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Commonly Used Terms for Year-End Adjustments in freee HR
漢字(Kanji) | 読み方(Hiragana) | English | Description |
年末調整 NenmatsuChosei | ねんまつちょうせい | Year-end Tax Adjustment | As described here |
本人情報 Honnin Joho | ほんにんじょうほう | Employee’s information | |
扶養状況 Fuyo Jyokyo | ふようじょうきょう | Dependent | |
同一生計配偶者 DoitsuSeikei Haiguusha | どういつせいけいはいぐうしゃ | Spouse whose living expenses are paid from the same resources (=employee)) | You are eligible for year-end tax deductions on freee HR only if you have selected the following:
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扶養親族 FuyoShinzoku | ふようしんぞく | Dependent whose living expenses are paid from the same resources (=employee)) | You are eligible for year-end tax deductions on freee HR only if you have selected the following
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収入 Shunyu | しゅうにゅう | Salary | Amount of salary before deduction |
合計所得金額 Goukei Shotoku kingaku | ごうけいしょとくきんがく | Total Amount of Income | Amount of income after deduction |
結婚状況 Kekkon Jokyo | けっこんじょうきょう | Marital Status | “Yes” means “currently married” “No” means “currently not married” |
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STEP3
Check your insurance premiums
STEP2
Verify your family information
STEP4
Check your morgtage
STEP1
Verify your identity
STEP5
Verify your income
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To start the process, please review and input the following personal details by following the on-screen instructions.
① Basic information
② Address on resident’s card
③ Other situations（Widow/single parent, disabled, married, working student, foreigner）
④ My Number（freee My Number Management will open）
⑤ Submit and confirm
⑥ Complete
Please review the information for accuracy and proceed to submit the completed form.
For further details, refer to the Help Page here.
STEP1: Verify your identity
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You will be redirected to freee My Number Management. Please register only the My Number of yourself and your dependent family members.
How to Register your My Number
①Click on the one marked “not been registered.”
②Please input your My Number (personal number), upload the documents verifying your number, and then click “Register”.
③Your number has been successfully registered if you see the message, "My number has been completed."
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STEP3
Check your insurance premiums
STEP2
Verify your family information
STEP4
Check your morgtage
STEP1
Verify your identity
STEP5
Verify your income
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Continue to check your Head of Household and Family Information.
Even if you do not have any dependents, be sure to check all the information until the last step and click the “Submit” button.
Please input the following information accordingly:
①Relationship to the head of household
②Name of head of household（When ① is other than the person who is applying）
*Please be sure to provide information here about the head of household as shown on your Certificate of Residence（住民票）
All registered family members are displayed in the Family Information section.
Please make sure that the information displayed is correct, including the most recent dependency status.
For further details, refer to the Help Page here.
Verify your family information ① Head of Household & Family Information
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The next step is to verify your income for your family members.
For spouse, provide the employment income and non-salary income for the current year; for dependents other than spouses, provide the income for the current year.
Please note the following:
For further details, refer to the Help Page here.
Verify your family information② Family Income
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For the next step, register your family member's My Number.
Please note that, in principle, only dependent family members are required to register their own My Number here.
For more information on how to register your My Number, please refer to this slide.
Once you have completed the registration up to this point, please review the information and submit the “Family Information” section.
Verify your family information③ Family My Number
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Flat Amount Tax Cut in freee HR
Spouses and relatives who are living in the same household are eligible for the flat amount cut of tax (定額減税) if certain requirements are met. For details, see National Tax Agency's Flat Amount Tax Reduction Site (in Japanese only) On the freee HR, a registered family member is eligible for a flat-amount tax cut (annual tax reduction) if all of the following apply:
POINT
Is my family eligible for the flat-amount cut of personal income tax (annual tax reduction)?
Required only for the year 2024
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Reference: Difference Between “Income” and “ Earnings” in Year-End Adjustment
Income (収入)
Earnings (所得)
This refers to the total amount paid before taxes and social insurance premiums are deducted. For salary income, this corresponds to the “amount paid” ① on the withholding tax slip.
This refers to the amount after deductions are made from your income. For salary income, it is the “amount after deduction of employment income” (②) on the withholding tax slip. ( If you have income other than salary, the “income” is the amount after deducting necessary expenses, etc.)（See details here）
① ②
Estimated Salary Income and Employment Earnings
Income | Earnings |
2,010,000 yen | 1,330,000yen |
1,500,000 yen | 950,000yen |
1,300,000 yen | 750,000yen |
1,060,000 yen | 510,000yen |
1,030,000 yen | 480,000yen |
↑Receive a flat-amount tax cut from family's own paycheck (not reflected in flat-amount tax cut amount).
↓Eligible to receive a flat-amount tax cut as a family member of yours.
Your family qualifies for the flat-amount tax cut, if your family member’s “earnings” are less than 480,000 yen.
Required only for the year 2024 (applied to certain cases)
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STEP3
Check your insurance premiums
STEP2
Verify your family information
STEP4
Check your morgtage
STEP1
Verify your identity
STEP5
Verify your income
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Next, review the information related to your insurance premiums.
①If you are using an electronic deductible certificate (XML file) downloaded from an insurance company's website or other source, please upload the file from the screen on the left.
②If you are using the printed paper premium deduction certificate that you received in the mail from your insurance company, please have it ready at hand and fill in the required information. The original paper certificate must be submitted to your company, so please follow the instructions from your administrator.
For further details, refer to the Help Page here .
Check your insurance premiums- Prepare & Input Insurance Premium Deduction Certificate Information
Example of a certificate of deduction for insurance premiums
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STEP3
Check your insurance premiums
STEP2
Verify your family information
STEP4
Check your morgtage
STEP1
Verify your identity
STEP5
Verify your income
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For this step, you will be reviewing information related to your mortgage. Please prepare the following documents and fill in the required information.
・Certificate of Special Tax Deduction for Housing Loans
Documents are mailed (or delivered electronically) by the tax office around October of the year in which you file your tax return to receive mortgage deductions for several years at a time. If you have lost the documents, you will need to apply to the tax office for reissuance. (For details, please refer to the National Tax Agency website.)
・Certificate of the year-end balance of the loan for home acquisition
This document is mailed around October each year from your financial institution where you have a mortgage loan.
For further details, refer to the Help Page here .
Check your mortgage - Prepare & Input Mortgage Deduction Certificate Information
Example of Certificate of Special Housing Loan Deduction (Mortgage Deduction Certificate)
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STEP3
Check your insurance premiums
STEP2
Verify your family information
STEP4
Check your morgtage
STEP1
Verify your identity
STEP5
Verify your income
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Next, you will check information regarding your income.
Provide this information if you had income other than your current income or salary this year (January-December). Please refer to the withholding tax slips (源泉徴収票) or other documents you received from your previous employer.
Items that must be listed as income other than current employment
・Main salary (A) income
For cases where you have income from a previous job, such as if you changed jobs and joined a new company during the current year (only if you were earning your primary salary)
Income from a second job (secondary salary that is B) or other earnings outside of salary
For details regarding earnings, please refer to this slide
Verify Your Income - Input Income/Income Other Than Current Employment
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Once your withholding tax slip is published by your HR, you will receive a notification and be able to download a copy.
*Some plans cannot provide withholding tax slips. If you apply to those cases, please receive your slip from your administrator.
For further details, refer to the Help Page here .
Steps to Follow After Completing Year-End Adjustment
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You have now successfully completed your year-end tax adjustment.
Great work!
Disclaimer: This is a provisional translation, and therefore, no responsibility or liability will be assumed for its accuracy, completeness, or use. The original document in Japanese should be referred to for any authoritative interpretation or legal reliance.
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