Summary
If you make 104,012,160 円 a year living in Japan, you will be taxed 43,889,738 円. That means that your net pay will be 60,122,422 円 per year, or 5,010,202 円 per month. Your average tax rate is 42.2% 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.