Mayor Gavin Newsom is the city's leader, but he is its 29th highest paid employee, more than a third of which earned more than $100,000 last year.
Newsom, whose salary is $250,903, is one of 9,487 workers who earned more than $100,000 last year, including overtime.
Top earner Charles Keohane, a former deputy police chief who earned $516,118, retired last year cashing out stored-up vacation, sick days and comp time.
The highest salary of the nearly 27,000 workers is $332,489, earned by Nathaniel Ford, head of the Municipal Transportation Agency.
Steve Falk, city Chamber of Commerce president and CEO, says state employment data show city workers average 20 percent more pay than the city's private sector.