Although a Wisbech Town existed in the 1890s, the current club was established in 1920 by the merger of three local clubs. They initially played in the Peterborough & District League, winning it in 1924–25, 1927–28, 1928–29, 1931–32 and 1932–33. In 1935 the club turned semi-professional and joined the United Counties League. Former West Ham player Sam Jennings was the first major signing, and the club won the United Counties League Cup in their first season.
In 1945–46 the club reached the first round of the FA Cup, but lost to Ipswich Town. The following season they won the league title, a feat repeated the season after. In 1950 they switched to the Eastern Counties League, before joining the Midland League in 1952.
In 1957–58 the club reached the second round of the FA Cup, beating Colchester United 1–0 in the first leg, before losing 2–1 at Reading. That season they finished second in the league, and switched again to the Southern League, joining the North-West Division. After finishing ninth and reaching the first round of the FA Cup again (losing 4–1 in a replay at Newport County), the club was placed in the new Premier Division as the league reorganised. They reached the first round again in 1959–60, but lost 4–1 to Wycombe Wanderers. They were relegated in 1960–61, but returned as Division One champions in 1961–62. Despite reaching the first round of the FA Cup again, they were relegated back to Division One in 1964–65. In 1965–66 they reached the first round of the FA Cup for the last time until 1995, losing 10–1 at Brighton, their record defeat.
In 1970 the club returned to the Eastern Counties League. They won the League Cup in 1971, the league and cup double in 1971–72, and the league again in 1976–77. In 1983–84 the club went 37 league matches unbeaten, but lost the title on goal difference. The following season they reached the semi-finals of the FA Vase, but lost to Halesowen Town in a semi-final replay after a draw over the original two legs. They reached the same stage the next season, but lost to Southall. They won the East Anglian Cup in 1988, and in 1990–91 they won the league again, and in 1995 the league cup.
In 1995–96 the club reached the first round of the FA Cup for the first time since the 1960s, but lost 5–1 at Kingstonian. However, after finishing second in the league that season the club were promoted to the Midland Division of the Southern League. Whilst playing in the Southern League, the club's reserve team entered the Eastern Counties League. The club reached the first round of the FA Cup again in 1996–97, losing 2–1 at home to St Albans City. The following season they reached the second round, after beating Billericay Town 2–1, before losing 2–0 at home to Bristol Rovers.
The club were relegated back to the Eastern Counties League in 2001–02 after finishing bottom of their division, and the reserve team dropped into the Cambridgeshire League.
Having finished the 2012–13 season in second place in the Eastern Counties League Premier Division, the club were eligible for promotion. However, this opportunity was declined in favour of a voluntary lateral movement, rejoining the United Counties League Premier Division instead. They were runners-up in 2017–18, earning promotion to Division One East of the Northern Premier League.