The 1987–88 season was Colchester United's 46th season in their history and seventh consecutive season in fourth tier of English football, the Fourth Division. Alongside competing in the Fourth Division, the club also participated in the FA Cup, the League Cup and the Associate Members' Cup. After a promising start to the season under Mike Walker, a disagreement between him and chairman Jonathan Crisp saw Walker leave Layer Road and in his place Roger Brown was recruited. From joint top of the table, Brown's side won just five games in the second half of the season to finish the season ninth.