Summary
If you make 99,428,676 円 a year living in Japan, you will be taxed 41,776,424 円. That means that your net pay will be 57,652,252 円 per year, or 4,804,354 円 per month. Your average tax rate is 42.0% and your marginal tax rate is 46.1%. 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 46.10 円, hence, your net pay will only increase by 53.90 円.
Bonus Example
A 1,000 円 bonus will generate an extra 539 円 of net incomes. A 5,000 円 bonus will generate an extra 2,695 円 of net incomes.