Due to the continued suspension of the Football League during the 1945–46 season, FA Cup matches from the first round through to the quarter-finals were played over two legs, in order to increase the number of – and income from – fixtures during the reduced campaign.

In a hard-fought first leg at The Dell, the Saints defeated County 4–3 thanks to goals from Ted Bates, Jack Bradley, Doug McGibbon and Don Roper.

[2] In the return leg at Newport's Somerton Park five days later, the Hampshire club once again edged out the Second Division newcomers, winning 2–1 thanks to goals from McGibbon and Bobby Veck.

[2] Aside from the FA Cup and the "unofficial" Football League South competition, Southampton played an additional three fixtures during the 1945–46 season.

The first was a friendly against Bournemouth & Boscombe Athletic on 2 May 1945, which the Saints won 3–1 thanks to goals from guest player John Sherratt and outside-forward Bobby Veck.