The 1979–80 season was Colchester United's 38th season in their history and third successive season in third tier of English football, the Third Division. Alongside competing in the Third Division, the club also participated in the FA Cup and the League Cup. An excellent season in the league took Colchester to their highest finish since the 1956–57 season with fifth position, having occupied the top four spots for the majority of the campaign. Colchester exited the FA Cup in round three to Reading, while they fell to defeat after a penalty shoot-out to First Division side Aston Villa.