During the 2008–09 season Cowdenbeath competed in the Scottish Third Division, Scottish Cup, Scottish League Cup and the Challenge Cup.
Cowdenbeath finished second in the Third Division,[1] entering the play-offs losing 5–4 on penalties to Stenhousemuir.
[2] Following Livingston's demotion after going into Administration, Cowdenbeath were promoted to the Second Division.
[3][4] They reached the second round of the Scottish Cup,[5] the second round of the League Cup[6] and were eliminated in the Quarter-finals of the Challenge Cup.
[7] For season 2008–09 Cowdenbeath were managed by Danny Lennon, following the sacking of Brian Welsh in the summer.