Why a bonus looks taxed harder than your salary
A bonus is not taxed at a higher rate than the rest of your pay. It is withheld differently. Your salary goes through the tables that read your Form W-4 and spread the year's tax evenly across your paychecks. A bonus paid on its own usually skips those tables: the employer takes a flat federal rate off the top, whatever your filing status, children or other income, and the state does the same under its own rule.
That flat rate is a convenience for payroll, not a statement about what you owe. For some people it is more than the bonus adds to their tax for the year, and the difference comes back when they file. For others, typically anyone whose salary already sits in a higher bracket, it is less, and the difference is due at filing. The comparison under the result shows which side of that line you are on and by how much.
The flat rate and the aggregate method
Federal rules give an employer two ways to withhold on a bonus paid separately from your salary. The first is the flat supplemental rate this page uses: one percentage of the bonus, no tables, no W-4. It is the usual choice for a bonus with its own payslip, and the rates it applies are listed in the rules table on this page, with the higher rate that is compulsory on the part of a year's supplemental pay above a set threshold.
The second is the aggregate method. The employer adds the bonus to a regular paycheck, withholds on the total as if that were your normal pay for the period, and takes off what the paycheck alone would have had withheld. Because the tables annualise whatever they are given, a large bonus run this way is treated for one pay period as though you earned that much every period, which is why aggregate withholding on a bonus can be startlingly high. It evens out on the return like everything else. If your bonus arrived inside a normal paycheck with no separate line for it, this is probably the method your employer used, and the federal line here will not match your payslip.
Social Security and Medicare on a bonus
A bonus is wages, so Social Security and Medicare apply to it exactly as they do to salary. Social Security stops once an employer has paid you the wage base for the year, and it counts per employer. That is why the page asks what this employer has already paid you: a bonus paid in December after a large salary may carry no Social Security at all, while the same bonus paid in March carries the full rate.
Medicare has no ceiling, and an extra Additional Medicare charge starts once one employer has paid you more than a set amount in the year. Employers must start withholding it at that point whatever your filing status, even though the threshold on the return itself depends on whether you file jointly. The payslip figure and the return can therefore differ, and the return is where it is settled.
What the state takes
Every state that taxes wages says something about bonuses, and they do not say the same thing. Some publish a flat supplemental rate, sometimes optional and sometimes compulsory, and California goes further with a separate rate for bonuses and stock options. Others have no flat rate at all and expect the bonus to go through the regular tables, added to a pay packet. States with no income tax on wages withhold nothing for income tax, though a few still charge disability, paid leave or long-term care contributions on every wage, bonus included.
The table of states on this page gives each state's rule for the tax year shown, and each state's name links to the employer publication the rule comes from. Where a state lets the employer choose between its flat rate and its regular tables, the calculation uses the flat rate, because that is what a separately paid bonus normally gets.
Reading the comparison
The second table sets the income tax withheld from the bonus against what the bonus adds to your tax for the year. That second figure is the regular annual calculation run twice, once with the bonus in the year's wages and once without, and the difference between the two. Nothing is estimated: it is the same calculation this site uses for a full year's salary, applied to two salaries.
For federal income tax that difference is the tax on your return, as long as this job is your only income and you take the standard deduction, because the annual withholding table is the tax rate schedule shifted by the standard deduction. With other income, itemized deductions or a working spouse the return will differ, and the figure is a guide rather than a bill. The rate beside it is the bonus's own rate at the margin, the number to hold against the flat rate.