For the only time in the history of the competition, all matches from the first round proper up to and including the sixth round proper were played over two legs, the first leg being played at the stadium of the team named first on the date specified for each round, which was always a Saturday. In the first and second rounds proper, the second leg was played on the following Saturday; from the third round onwards, it was played during the week following the first leg. If aggregate scores were level after 90 minutes of the second leg had been played, a replay would take place at a neutral venue. These changes were made in order to give clubs additional revenue, as the Football League would not resume normal play until the autumn of 1946.
Calendar
Round
Date
Extra preliminary round
Saturday 1 September 1945
Preliminary round
Saturday 8 September 1945
First round qualifying
Saturday 22 September 1945
Second round qualifying
Saturday 6 October 1945
Third round qualifying
Saturday 20 October 1945
Fourth round qualifying
Saturday 3 November 1945
First round proper
Saturday 17 November 1945 Saturday 24 November 1945
Second round proper
Saturday 8 December 1945 Saturday 15 December 1945
Third round proper
Saturday 5 January 1946 w/c Monday 7 January 1946
Fourth round proper
Saturday 26 January 1946 w/c Monday 28 January 1946
Fifth round proper
Saturday 9 February 1946 w/c Monday 11 February 1946
Sixth round proper
Saturday 2 March 1946 w/c Monday 4 March 1946
Semi-finals
Saturday 23 March 1946
Final
Saturday 27 April 1946
w/c = week commencing
Qualifying rounds
As with the 1919–20 tournament, participant numbers were down this season after many clubs from the lower echelons of the English football system did not resume after the Second World War. Local leagues across the UK were reeling after seven seasons of competitive hiatus, while other stronger clubs such as Burton Town were unable to survive the loss of regular income streams during wartime.
Most of the clubs from outside the Football League who did enter the tournament still competed in the qualifying rounds to secure one of 25 places available in the first round proper.
Advancing to the competition proper for the first time were Willington, Netherfield, Wisbech Town, Slough United, Sutton United, Trowbridge Town and Lovell's Athletic, while Shrewsbury Town had not done so since 1909–10. Slough United's appearance in the first round was also the first by a team from that town since Swifts had been knocked out by The Wednesday in 1889-90.
This season's extra preliminary round contained only eight teams (four from Oxfordshire and two each from Buckinghamshire and Middlesex). None of those progressed past the second qualifying round. Barnet, Slough United and Sutton United were the only clubs to progress to the first round proper from the preliminary round.
The first leg matches were played on Saturday, 17 November 1945 and the second legs on the following Saturday, 24 November 1945. No replays were necessary.
The first leg matches were played on Saturday, 8 December 1945 and the second legs on the following Saturday, 15 December 1945. No replays were necessary.
The first leg matches were played on Saturday, 5 January 1946 and the second legs in the following week commencing Monday, 7 January 1946. Two replays were necessary, both of which were played on Wednesday, 16 January 1946. Lovell's Athletic was the last non-league club left in the competition.
The first leg matches were played on Saturday, 26 January 1946 and the second legs in the following week commencing Monday, 28 January 1946. One replay was necessary, which was played on 4 February 1946.