The 2016–17 season was Colchester United's 80th season in their history and their first season competing in League Two following their relegation from League One in the 2015–16 season. It was their first season in the fourth tier of English football for 18-years. Along with competing in League Two, the club also participated in the FA Cup, EFL Cup and EFL Trophy. In the cup competitions, the U's were defeated in the first round of the EFL Cup and FA Cup by Brighton & Hove Albion and Chesterfield respectively, while they finished bottom of their group in the revamped EFL Trophy competition.