The 2013–14 season is Colchester United's sixth consecutive season in the third tier of English football following survival from relegation to League Two on the final day of the 2012–13 season. It will also be manager Joe Dunne's first full season in charge of the club after taking over from John Ward in September 2012. Dunne led his side to a 16th position league finish, though it took until the penultimate game of the season to secure their League One status for another season.

After narrowly avoiding relegation to League Two on the final day of the 2012–13 season, manager Joe Dunne began strengthening the team early in pre-season by signing former loanee Craig Eastmond from Arsenal. Eastmond had featured for Colchester in the previous season before injury cut his stint short, but returned to the Community Stadium following the expiration of his contract with the Gunners, signing a two-year deal. Dunne had already allowed Matt Heath and Jackson Ramm leave the club after their contracts with the club had expired. The development squad was bolstered first by the signing of Milton Keynes Dons youth-team product Mason Spence and the news that Freddie Ladapo had signed a new one-year contract to remain at the club. Goalkeeper and former youth-team player Mark Cousins also extended his stay with the club, penning a new one-year contract on 14 June.

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