Summary
If you make 2,063,984 円 a year living in Japan, you will be taxed 386,820 円. That means that your net pay will be 1,677,164 円 per year, or 139,764 円 per month. Your average tax rate is 18.7% and your marginal tax rate is 20.5%. 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 20.52 円, hence, your net pay will only increase by 79.48 円.
Bonus Example
A 1,000 円 bonus will generate an extra 795 円 of net incomes. A 5,000 円 bonus will generate an extra 3,974 円 of net incomes.