Option 1. The employer may withhold a flat 25% for federal income taxes from the bonus payment. If the employee receives over $1 million in bonus payments in one year, the employer can withhold 35% from the amount over $1 million in addition to 25% of the first $1 million.Option 2.owever, seems to me that your bonus is not $1,200 but is $984 as $984 is what is showing up on your pay stub. As I stated before – the IRS play by the “You can pay me now or you can pay me later rules” – your bonus just gets added with normal income to determine how much you owe the IRS.