Summary
If you make 9,913,908 円 a year living in Japan, you will be taxed 2,621,589 円. That means that your net pay will be 7,292,319 円 per year, or 607,693 円 per month. Your average tax rate is 26.4% and your marginal tax rate is 33.1%. This marginal tax rate means that your immediate additional income will be taxed at this rate. For instance, an increase of 100 円 in your salary will be taxed 33.09 円, hence, your net pay will only increase by 66.91 円.
Bonus Example
A 1,000 円 bonus will generate an extra 669 円 of net incomes. A 5,000 円 bonus will generate an extra 3,346 円 of net incomes.