The 2006–07 Football League Trophy, known as the 2006–07 Johnstone's Paint Trophy for sponsorship reasons, was the 23rd staging of the Football League Trophy, a knockout competition for English football clubs in Leagues One and Two. The winners were Doncaster Rovers from League One and the runners-up were Bristol Rovers from League Two. Swansea City were the defending champions, but lost to Peterborough United in the second round.