The season was most notable for Colchester's run in the FA Cup, where they defeated three Football League clubs as they progressed to the fifth round, before being beaten 5–0 by First Division side Blackpool.

Manager Ted Fenton's first-team squad had featured 28 part-time professionals during the 1946–47 season, but this number was reduced to 17 for the 1947–48 campaign, while signings such as Bob Allen and Harry Bearryman, and the emergence of Vic Keeble bolstered the ranks.

The competition began with a 3–2 win over league rivals Chelmsford City in the fourth qualifying round in front of a Layer Road crowd of 10,396.

Third Division North side Wrexham visited Layer Road for the second round match, with the visitors falling to a 1–0 defeat courtesy of a Bob Curry goal in front of a 10,642 crowd.

With the increased interest in Colchester's cup heroics, the crowd from the previous game could have trebled had Layer Road been able to accommodate the fans.

Not since pre-war Illumination weekends has there been such an invasion as stormed our streets from 4 o'clock this morning.Despite the good natured support, the home team defeated the U's by 5–0 in front of a sell-out 29,500 Bloomfield Road crowd.

However, the FA Cup success had an effect on Colchester's league form, with the club eventually finishing fourth, nine points adrift of champions Merthyr Tydfil.