South Hetton, County Durham born goalkeeper Fred Thompson began his football career with Sunderland West End in 1894 before moving to First Division Sunderland in August 1895, where he was understudy to the legendary Ned Doig, making his Football League debut at Burnley that September, one of only two appearances he made for The Wearsiders. In July 1896 he moved to Bury,, where he was understudy to Archie Montgomery for his first three seasons at Gigg Lane, sharing duties with Montgomery in 1899-1900, when Thompson was in goal as Bury won the FA Cup, playing in all the FA Cup ties and helping to defeat Southern League Southampton 4-0 in the Final at The Crystal Palace. He became the principal goalkeeper in 1900-01, however Montgomery returned for the 1901-02 season, Thompson making only 4 appearances, and he joined Bolton Wanderers in May 1902 after 75 appearances for Bury over his 6 years at the club.
He made 21 appearances for Bolton in 1902-03 but lost his place to the emerging Dai Davies, joining Southern League Luton Town in the 1903 close season. He joined Portsmouth in 1904, playing 9 times for Pompey before moving to Fulham in May 1905, helping them to win the Southern League Championship in 1905-06 before joining Norwich City. He had two seasons in East Anglia before signing for Doncaster Rovers in 1908, joining Denaby United in 1909 and Brodsworth Main Colliery in 1911 before his eventual retirement.