Stockton FC changed its name in 1999/2000 season to Thornaby-on-Tees FC and for the 2000/01 season its name again to Thornaby F.C.

Thornaby FC joined the Northern League first division for season 2003/04 as the were promoted from the second division.

The orginal Stockton and Athletic Football club was formed in 1882 & over 50 years won many honours in the Northern league until due to finacial problem, the Club was disbanded, in 1975, and Victoria ground was sold.

The new club was formed in 1980 when a successful Stockton and District League side, Stockton Cricket Club, changed its name. Stockton FC were elected to the Wearside League in 1980/81 season. They spent two seasons at Grangefield Youth and Community Centre before moving to Tilery Recreation Centre. In 1982/83 the club reached the final of the Sunderland Shipowners Cup and won the league Sportsmanship Cup.

Stockton FC were elected to the Northern League in 1985 & won the second division Championship in 1987/88.

Thornaby-on-Tees was born in the new millennium, but after being relegated in 2000/01, changed its name to Thornaby F.C. & swiftly returned to the First Division. The manager Trevor Arnold and his company K Home Engineering is the main sponsor of Thornaby F.C. Thornby were relegated again but in season 2003/04 moved back up to the First Division.