Founded in 1884, Lincoln won the Midland League in 1889–90, their first full season playing league football. They moved on from the Football Alliance to become founder members of the Football League Second Division in 1892, remaining there until they failed re-election in 1908. They won immediate re-election after winning the next year's Midland League, and would repeat this feat after failing re-election again in 1911 and 1920. Founder members of the Football League Third Division North in 1921, they won promotion as champions in 1931–32, but were relegated two seasons later. Crowned Third Division North champions again in 1947–48, they were relegated the next year, but would remain in the second tier for nine seasons after again winning the Third Division North title in 1951–52. Two successive relegations left them in the Fourth Division by 1962, where they would remain until Graham Taylor's title winning campaign of 1975–76.
Relegated in 1978–79, they secured promotion again two years later but suffered a double relegation to find themselves in the Conference by 1987. Lincoln made an immediate recovery however, regaining their Football League status with the Conference title in 1987–88. They were promoted again in 1997–98, but were relegated the next season. They reached the play-offs in five consecutive seasons, from 2002 to 2007, losing in the final twice (2002–03 and 2004–05) and the semi-finals three times, which is a competition record. However they exited the division at the other end when they were returned to the Conference after relegation at the end of the 2010–11 campaign. A six season stay in non-league was ended when Cowley brothers Nicky and Danny led the club to the National League title in 2016–17, as well as a run to the quarter-finals of the FA Cup – this made them the first non-league side to reach that stage in 103 years. Though they lost in the League Two play-offs the next year, they did win the 2018 EFL Trophy Final.