The club was originally established as Fletton United in 1901. They were founder members of the Peterborough & District League in 1902 and were its inaugural champions, remaining unbeaten in the league's first season. After retaining the league title in both of the next two seasons,[1] the club left the league and joined Division One of the Northamptonshire League.[2] They finished bottom of the league in 1913–14, but were runners-up in 1921–22.[2]
After finishing third in 1922–23, the club were voted into the Eastern Section of the Southern League, at which point they adopted the name Peterborough & Fletton United in an attempt to gain the backing of tradesmen and people of Peterborough, and give other Southern League clubs an idea of their geographical location.[3] In their first season in the league they won the Eastern Section, and went on to beat Yeovil 3–1 in the championship play-off.[4]In1927–28 they reached the third round of the FA Cup, where they lost 4–3 to Birmingham, having been 3–0 up.[5] At the end of the season they applied for the elections to Division Three South of the Football League, but received only two votes.[6]
After finishing eighth out of ten clubs in 1931–32 the club left the Southern League,[7] intending to join the East Midlands. However, with the club deep in financial trouble, on 6 August 1931 the Football Association suspended the club until it paid the £154 due in wages to players.[8] In November 1932 the club went into voluntary liquidation with debts of £1,750.[9]