Summary
If you make 2,063,988 円 a year living in Japan, you will be taxed 386,820 円. That means that your net pay will be 1,677,168 円 per year, or 139,764 円 per month. Your average tax rate is 18.7% and your marginal tax rate is 20.6%. 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 20.60 円, hence, your net pay will only increase by 79.40 円.
Bonus Example
A 1,000 円 bonus will generate an extra 794 円 of net incomes. A 5,000 円 bonus will generate an extra 3,970 円 of net incomes.