FSA chief executive John Tiner was paid £471,656 last year, a big rise from £361,904 in the previous year.
The total includes a basic salary of £310,971, a performance-related bonus of £52,000 and other benefits of £108,685, including £47,741 towards his pension.
The FSA says Tiner's increased salary this year reflects the additional responsibilities he took on when promoted from managing director to chief executive last September.
The second-highest earner after Tiner is adviser to the chairman and chief executive Michael Foot. He received £346,175 in 2004, up from £322,017 in 2003, which includes a £39,000 performance related bonus as well as £44,675 in other benefits.
Chairman Callum McCarthy was paid a salary of £314,000 but asked not to be a part of the performance-related bonus scheme.
Carol Sergeant, who was responsible for enforcement and fines at the regulator but who left in September last year to join Lloyds TSB as chief risk director, received remuneration of £254,347.
Non-executive directors at the FSA, who include HBOS group chief executive James Crosby and former Bradford & Bingley chief executive Christopher Rodrigues typically received £20,000.