The original Bootle F.C. were founder members of the Football Alliance in 1889. In 1890 the club reached the quarter-finals of the FA Cup, where they lost to Blackburn Rovers. When the Alliance merged with the Football League in 1892, Bootle became founder members of the new Second Division. However, the club dropped out after one season (and were replaced by neighbours Liverpool) and seemingly disappeared.

In 1953, a new Bootle F.C. was formed. In 1974, the club joined the Lancashire Combination, which they won in 1976 and 1977. They then joined the Second Division of the Cheshire County League, which they won in their first season, and were promoted to the First Division. In 1982 the Cheshire County League was one of the leagues that merged to form the North West Counties League, which Bootle duly joined, becoming a member of the First Division. The club spent most of their time in the First Division until 2000 when they dropped into the Second Division. However, despite finishing 6th in 2002, the club dropped into the Liverpool County Combination. In 2006 they were elected back into the North West Counties league.