Layer Road's Clock End received a makeover during the off season, with a new covered and all seated stand in place.

In the League Cup, Colchester overturned a 3–2 first leg deficit against West Bromwich Albion into victory with a 3–1 win at The Hawthorns with Steve Whitton in goal for the entire second half following an injury to goalkeeper Garrett Caldwell.

Paul Buckle scored Colchester's first-ever golden goal in the Football League Trophy against Millwall following a first round win against Cambridge United.

In the final with 45,077 in attendance, neither side could find a breakthrough, and the tie went to extra time following a goalless 90 minutes.

The U's took the lead in the shoot-out after Owen Archdeacon missed Carlisle's second effort, but consecutive misses from youth team product Karl Duguid and Peter Cawley meant that Steve Hayward's converted effort won the shoot-out for Carlisle 4–3.