The club was established in 1883 and joined the
Peterborough & District League in 1911. Although they left the league in 1929, they returned the following season and were Division One champions in 1933–34. In 1947 they joined the
United Counties League, but struggled in the new league, finishing second-from-bottom in 1948–49 and 1949–50, bottom in 1953–54 and second-from-bottom again in 1954–55 and 1955–56. After leaving the league in 1956, they rejoined the Peterborough & District League, before switching to Division One South of the
Central Alliance in 1958. Bourne won Division One South in 1959–60, In 2024–25 Bourne were Premier Division North runners-up, qualifying for the promotion play-offs. After beating
AFC Mansfield 4–0 in the semi-finals, they defeated
Boston Town 8–7 on penalties in the final to earn promotion to Division One Midlands of the
Northern Premier League.
Other teams The reserve team has competed in the Peterborough & District League, the
Lincolnshire League and the United Counties League. Between 1952 and 1956 the club also entered an 'A' Team in the Peterborough & District League. The 'A' Team was resurrected at the start of the 2022–23 season and rejoined the Peterborough & District League, playing at Elsea Park. After winning back-to-back league titles the 'A' Team merged with the reserve team for the 2024–25 season and achieved a third consecutive promotion. ==Ground==