The 2006–07 season was Leyton Orient's 108th season and their 91st in the Football League.
It was their first season back in the third tier of the English football league system, Football League One, following promotion in the 2005–06 season.
Orient avoided relegation from League One, finishing 20th, and also took part in the FA Cup, League Cup, Football League Trophy, but were eliminated in the first round of the FA Cup and Football League Trophy, and the first round of the League Cup.