The war in Europe has ended by the time that the 1945-46 season arrives, but the Football League decides that they will allow clubs the grace of the season to put their affairs in order and recruit a playing staff over the next year, with the aim of restarting professional football in August 1946. Therefore, the Wartime Leagues continue for another season, and this allows Cyril Spiers to put together what is to become the 1946-47 'local heroes' side. Three players return after being taken prisoner by the Japanese, but their physical condition is not good. Of the three, Billy Baker stands the best chance of recovery, but Bobby Tobin and Billy James have had their health badly damaged. Ken Hollyman returns from the armed forces to resume his football career, while Cyril Spiers signs two more influential players in the post war years when Bryn Allen transfers from Swansea Town and Stan Richards signs from a junior side called Tufnell Park. The F.A. decide to play the F.A.Cup in a unique format for the competition, over two legs in each round. City are drawn against West Bromwich Albion and go out on aggregate 1-5. On November 17th, City have one of their most famous games when they entertain Moscow Dynamo. City get a beating by 1-10. However, the aim of the season has been realised, City have a small squad of professional players carefully assembled by Cyril Spiers and are ready for the resumption of full time football. However, in a shock move, Cyril Spiers resigns before the season ends reportedly over disagreement involving his salary.
MANAGER: Cyril Spiers (Resigned 7 April 1946)
| Date | Opponents | Competition | V. | Res. | Goalscorers | Att. | |
| August 14 | Swansea Town | Friendly | H | 4-3 | W | Carless 2, Rees 2 | 2,000 |
| August 18 | League West XI | Friendly | H | 2-0 | W | Rees, Gibson | 1,000 |
| August 25 | Bournemouth & B.A. | 3rd Division(S) - South Division | H | 9-3 | W | Rees 4, Clarke 2, Gibson, Carless | 10,000 |
| September 1 | Bournemouth & B.A. | 3rd Division(S) - South Division | A | 5-1 | W | Rees, Clarke 3, Wood | 7,000 |
| September 8 | Torquay United | 3rd Division(S) - South Division | H | 6-0 | W | Clarke, Wood, Carless, Rees 2, Gibson | 12,000 |
| September 12 | Crystal Palace | 3rd Division(S) - South Division | A | 0-3 | L | 5,000 | |
| September 15 | Torquay United | 3rd Division(S) - South Division | A | 7-0 | W | Spencer (og), Lester, Rees 3, Clarke 2 | 2,200 |
| September 22 | Aldershot | 3rd Division(S) - South Division | H | 4-1 | W | Rees 2, Carless, Wood | 16,000 |
| September 29 | Aldershot | 3rd Division(S) - South Division | A | 5-1 | W | Rees, Moore, Clarke, Carless, Hollyman | 4,000 |
| October 6 | Bristol City | 3rd Division(S) - South Division | A | 2-3 | L | Moore, Rees | 18,711 |
| October 13 | Bristol City | 3rd Division(S) - South Division | H | 2-4 | L | Rees, Clarke | 28,000 |
| October 20 | Brighton & H.A. | 3rd Division(S) - South Division | H | 4-0 | W | Clarke, Rees 2, Reece (og) | 22,000 |
| October 27 | Brighton & H.A. | 3rd Division(S) - South Division | A | 3-2 | W | Moore, Gibson, Clarke | 8,500 |
| November 3 | Exeter City | 3rd Division(S) - South Division | A | 2-3 | L | Gibson, Clarke | 6,341 |
| November 10 | Exeter City | 3rd Division(S) - South Division | H | 0-0 | D | 18,000 | |
| November 17 | Dynamo Moscow | Friendly | H | 1-10 | L | Moore | 31,000 |
| December 1 | Swindon Town | 3rd Division(S) - South Division | A | 2-1 | W | Wood, Kelso (og) | 11,876 |
| December 8 | Swindon Town | 3rd Division(S) - South Division | H | 3-0 | W | Lever, Clarke, Wood | 6,000 |
| December 15 | Reading | 3rd Division(S) - South Division | H | 2-1 | W | Wood 2 | 8,000 |
| December 22 | Reading | 3rd Division(S) - South Division | A | 1-3 | L | Rees | 5,295 |
| December 25 | Bristol Rovers | 3rd Division(S) - South Division | A | 2-2 | D | 8,000 | |
| December 26 | Bristol Rovers | 3rd Division(S) - South Division | H | 4-2 | W | Allen, Hollyman, Clarke 2 | 18,000 |
| December 29 | Crystal Palace | 3rd Division(S) - South Division | H | 6-2 | W | Wright 2, Allen 2, Hollyman 2 | 25,000 |
| January 12 | Watford | 3rd Division(S) Cup (Q) | A | 7-1 | W | Clarke 2, Wright 2, Allen 2, Tennant | 7,800 |
| January 19 | Watford | 3rd Division(S) Cup (Q) | H | 0-2 | L | 14,000 | |
| January 26 | Exeter City | 3rd Division(S) Cup (Q) | A | 1-2 | L | Haddon | 8,000 |
| February 2 | Exeter City | 3rd Division(S) Cup (Q) | H | 5-1 | W | Rees 2, Wright, Lever, Clarke | 15,000 |
| February 9 | Torquay United | 3rd Division(S) Cup (Q) | A | 0-1 | L | 4,000 | |
| February 16 | Torquay United | 3rd Division(S) Cup (Q) | H | 3-0 | W | Allen, Rees 2 | 14,700 |
| February 23 | Bristol Rovers | 3rd Division(S) Cup (Q) | A | 0-1 | L | 11,200 | |
| March 2 | Bristol Rovers | 3rd Division(S) Cup (Q) | H | 3-0 | W | Richards 3 | 18,000 |
| March 9 | Bristol City | 3rd Division(S) Cup (Q) | A | 2-3 | L | Hollyman, Allen | 17,375 |
| March 16 | Bristol City | 3rd Division(S) Cup (Q) | H | 3-2 | W | Hill 2, Allen | 19,000 |
| March 23 | Swindon Town | 3rd Division(S) Cup (Q) | A | 2-3 | L | Rees, Moore | 11,779 |
| March 30 | Swindon Town | 3rd Division(S) Cup (Q) | H | 2-0 | W | Allen 2 | 19,500 |
| April 6 | Reading | 3rd Division(S) Cup (Q) | A | 2-3 | L | Clarke, Richards | 11,000 |
| April 10 | Combined BAOR XI | Friendly | N* | 1-1 | D | Rees | 15,000 |
| April 13 | Reading | 3rd Division(S) Cup (Q) | H | 5-2 | W | Richards 2, Rees, Clarke, Gibson | 21,500 |
| April 20 | Crystal Palace | 3rd Division(S) Cup (Q) | A | 3-0 | W | Clarke | 17,500 |
| April 27 | Crystal Palace | 3rd Division(S) Cup (Q) | H | 1-1 | D | Allen, Hudghill (og), Rees | 29,000 |
| Notts County | Friendly | H | 5-1 | W | Clarke 2, Rees 2, Richards | 7,000 | |
| * Played in Brunswick |
Names displayed in light green indicate a player making his debut.
| No. | Date | Opponents | Competition | V. | Res. | Goalscorers | Att. | 1. | 2. | 3. | 4. | 5. | 6. | 7. | 8. | 9. | 10. | 11. | |
| 1. | January 5 | W.B.A. | FA Cup (3-1) | H | 1-1 | D | Allen | 33,000 | K.McLoughlin | A.Sherwood | M.Raybould | G.Wright | F.Stansfield | L.Lester | C.Gibson | K.Hollyman | B.Allen | T.Wood | R.Clarke |
| 2. | January 9 | W.B.A. | FA Cup (3-2) | A | 0-4 | L | 18,025 | K.McLoughlin | A.Sherwood | M.Raybould | G.Wright | F.Stansfield | K.Hollyman | B.Moore | B.Allen | W.Rees | T.Wood | R.Clarke |