Summary
If you make 42,181,944 円 a year living in Japan, you will be taxed 15,399,204 円. That means that your net pay will be 26,782,740 円 per year, or 2,231,895 円 per month. Your average tax rate is 36.5% and your marginal tax rate is 45.9%. 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 45.87 円, hence, your net pay will only increase by 54.13 円.
Bonus Example
A 1,000 円 bonus will generate an extra 541 円 of net incomes. A 5,000 円 bonus will generate an extra 2,707 円 of net incomes.