Summary
If you make 3,121,914 円 a year living in Japan, you will be taxed 622,015 円. That means that your net pay will be 2,499,899 円 per year, or 208,325 円 per month. Your average tax rate is 19.9% and your marginal tax rate is 23.1%. 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 23.11 円, hence, your net pay will only increase by 76.89 円.
Bonus Example
A 1,000 円 bonus will generate an extra 769 円 of net incomes. A 5,000 円 bonus will generate an extra 3,845 円 of net incomes.