The 1990–91 season was Colchester United's first season outside of the Football League since 1950, when they were elected to the football league. The season ended with Colchester finishing runners-up in the Conference behind Barnet by two points.

Lincoln and Darlington had both returned to the Football League at the first attempt from the Conference and the onus was on new Player Manager Ian Atkins to achieve the same. United remained full-time and wearing a navy and white striped kit enjoyed a 100% record from their first six home games.

Layer Road was sold back to the Council for £1.2m to help clear debts with the club leasing for a maximum of three seasons. Barnet and Kettering were U's main challengers and it took until April for U's to hit top spot.

United faced the ignominy of having to compete in the FA Cup Fourth Qualifying Round and had a shock home defeat to Witton Albion in the FA Trophy Quarter Finals after beating neighbours Wivenhoe Town.

Facing late challengers Altrincham drew a Layer Road crowd of 7,221, but a draw and Barnet's matching form meant that Colchester finished runners-up by two points. Chairman Jonathan Crisp fumed: "To come second with a fully professional squad in a part-time League is a bloody disgrace." He soon left the club, a wiser if not poorer man, as did Atkins who joined Birmingham as coach.

Note: Flags indicate national team as defined under FIFA eligibility rules. Players may hold more than one non-FIFA nationality.

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