The 1958–59 season was Colchester United's 17th season in their history and their ninth season in the third tier of English football, the newly formed national Third Division. Alongside competing in the Third Division, the club also participated in the FA Cup. Colchester reached the fourth round of the FA Cup, beating Bath City, Yeovil Town and Chesterfield on their way to meeting Arsenal. Drawn at home, Colchester held Arsenal to a 2–2 Layer Road draw, but were defeated 4–0 at Highbury in the replay. Colchester finished fifth in the Third Division, nine points shy of promotion.