| D3PSFL2 | 16/05/1990 | Notts County | 2-0 | Bolton Wanderers | | | 15,200 | Loss |
| D3PSFL1 | 13/05/1990 | Bolton Wanderers | 1-1 | Notts County | Philliskirk (pen) | | 15,105 | Draw |
| D3 | 05/05/1990 | Swansea City | 0-0 | Bolton Wanderers | | | 5,623 | Draw |
| D3 | 01/05/1990 | Bolton Wanderers | 2-2 | Huddersfield Town | Green, Philliskirk (pen) | | 8,550 | Draw |
| D3 | 28/04/1990 | Bolton Wanderers | 1-0 | Bristol City | Green | | 11,098 | Win |
| D3 | 24/04/1990 | Bury | 2-0 | Bolton Wanderers | | | 6,551 | Loss |
| D3 | 21/04/1990 | Bolton Wanderers | 0-1 | Shrewsbury Town | | | 5,665 | Loss |
| D3 | 16/04/1990 | Blackpool | 2-1 | Bolton Wanderers | Philliskirk | | 5,435 | Loss |
| D3 | 14/04/1990 | Bolton Wanderers | 1-1 | Tranmere Rovers | Storer | | 9,070 | Draw |
| D3 | 10/04/1990 | Walsall | 2-1 | Bolton Wanderers | Philliskirk (pen) | | 3,376 | Loss |
| D3 | 07/04/1990 | Bolton Wanderers | 2-1 | Preston North End | Philliskirk 2 | | 8,266 | Win |
| D3 | 03/04/1990 | Bolton Wanderers | 3-0 | Reading | Philliskirk 2, Thompson S | | 4,679 | Win |
| D3 | 31/03/1990 | Chester City | 2-0 | Bolton Wanderers | | | 2,738 | Loss |
| D3 | 27/03/1990 | Leyton Orient | 0-0 | Bolton Wanderers | | | 3,296 | Draw |
| D3 | 24/03/1990 | Bolton Wanderers | 0-1 | Brentford | | | 6,156 | Loss |
| D3 | 20/03/1990 | Bolton Wanderers | 0-0 | Crewe Alexandra | | | 7,241 | Draw |
| D3 | 16/03/1990 | Wigan Athletic | 2-0 | Bolton Wanderers | | | 6,850 | Loss |
| D3 | 10/03/1990 | Bolton Wanderers | 3-0 | Notts County | Darby, Philliskirk, Reeves | | 8,420 | Win |
| D3 | 05/03/1990 | Mansfield Town | 0-1 | Bolton Wanderers | Darby | | 3,334 | Win |
| D3 | 03/03/1990 | Reading | 2-0 | Bolton Wanderers | | | 4,461 | Loss |
| D3 | 24/02/1990 | Bolton Wanderers | 3-1 | Birmingham City | Reeves 2, Thompson S | | 7,618 | Win |
| AMCNSF | 20/02/1990 | Tranmere Rovers | 2-1 | Bolton Wanderers | Philliskirk | | 9,315 | Loss |
| D3 | 17/02/1990 | Northampton Town | 0-2 | Bolton Wanderers | Darby, Thompson S | | 3,432 | Win |
| D3 | 10/02/1990 | Bolton Wanderers | 0-2 | Rotherham United | | | 7,728 | Loss |
| AMCNQF | 31/01/1990 | Bolton Wanderers | 1-0 | Rotherham United | Storer | | 6,838 | Win |
| D3 | 28/01/1990 | Bristol Rovers | 1-1 | Bolton Wanderers | Philliskirk | | 7,722 | Draw |
| D3 | 20/01/1990 | Bolton Wanderers | 3-1 | Cardiff City | Philliskirk 2 (1 pen), Comstive | | 7,017 | Win |
| D3 | 13/01/1990 | Fulham | 2-2 | Bolton Wanderers | Pike, Storer | | 4,523 | Draw |
| AMCN1 | 09/01/1990 | Bolton Wanderers | 2-1 | Lincoln City | Reeves 2 | | 4,420 | Win |
| D3 | 06/01/1990 | Tranmere Rovers | 1-3 | Bolton Wanderers | Cowdrill, Darby, Storer | | 8,273 | Win |
| D3 | 30/12/1989 | Bolton Wanderers | 3-1 | Bury | Reeves 2, Storer | | 10,628 | Win |
| D3 | 26/12/1989 | Bolton Wanderers | 2-0 | Blackpool | Darby, Cowdrill | | 9,944 | Win |
| D3 | 16/12/1989 | Shrewsbury Town | 3-3 | Bolton Wanderers | Thompson S 2, Philliskirk | | 3,443 | Draw |
| AMCQ | 05/12/1989 | Wigan Athletic | 1-0 | Bolton Wanderers | | | 2,306 | Loss |
| D3 | 02/12/1989 | Bolton Wanderers | 0-3 | Northampton Town | | | 5,501 | Loss |
| AMCQ | 29/11/1989 | Bolton Wanderers | 2-0 | Crewe Alexandra | Darby, Brookman | | 3,868 | Win |
| D3 | 25/11/1989 | Birmingham City | 1-0 | Bolton Wanderers | | | 8,081 | Loss |
| LC3R3 | 21/11/1989 | Swindon Town | 2-1 | Bolton Wanderers | Came (aet) | | 11,238 | Loss |
| FAC1 | 18/11/1989 | Blackpool | 2-1 | Bolton Wanderers | Crombie | | 7,309 | Loss |
| LC3R2 | 14/11/1989 | Bolton Wanderers | 1-1 | Swindon Town | Philliskirk (pen) (aet) | | 14,129 | Draw |
| D3 | 11/11/1989 | Bristol City | 1-1 | Bolton Wanderers | Brown P | | 11,994 | Draw |
| LC3R | 07/11/1989 | Bolton Wanderers | 1-1 | Swindon Town | Brown P (aet) | | 11,533 | Draw |
| D3 | 04/11/1989 | Bolton Wanderers | 0-0 | Swansea City | | | 6,618 | Draw |
| D3 | 31/10/1989 | Bolton Wanderers | 1-1 | Walsall | Darby | | 7,363 | Draw |
| D3 | 28/10/1989 | Preston North End | 1-4 | Bolton Wanderers | Philliskirk, Thompson S, Darby, Kelly (og) | | 9,135 | Win |
| LC3 | 24/10/1989 | Swindon Town | 3-3 | Bolton Wanderers | Henshaw, Philliskirk, Came | | 8,318 | Draw |
| D3 | 21/10/1989 | Bolton Wanderers | 1-0 | Chester City | Philliskirk | | 6,496 | Win |
| D3 | 17/10/1989 | Brentford | 1-2 | Bolton Wanderers | Reeves 2 | | 4,537 | Win |
| D3 | 14/10/1989 | Crewe Alexandra | 2-2 | Bolton Wanderers | Reeves 2 | | 4,284 | Draw |
| D3 | 07/10/1989 | Bolton Wanderers | 3-2 | Wigan Athletic | Philliskirk (pen), Darby 2 | | 6,462 | Win |
| LC2L2 | 03/10/1989 | Watford | 1-1 | Bolton Wanderers | Comstive | | 8,452 | Draw |
| D3 | 30/09/1989 | Bolton Wanderers | 1-1 | Mansfield Town | Winstanley | | 5,797 | Draw |
| D3 | 26/09/1989 | Notts County | 2-1 | Bolton Wanderers | Philliskirk | | 5,392 | Loss |
| D3 | 23/09/1989 | Bolton Wanderers | 2-1 | Leyton Orient | Cowdrill, Philliskirk | | 5,951 | Win |
| LC2L1 | 19/09/1989 | Bolton Wanderers | 2-1 | Watford | Philliskirk 2 | | 6,856 | Win |
| D3 | 16/09/1989 | Rotherham United | 1-0 | Bolton Wanderers | | | 6,846 | Loss |
| D3 | 09/09/1989 | Bolton Wanderers | 1-0 | Bristol Rovers | Reeves | | 5,913 | Win |
| D3 | 02/09/1989 | Huddersfield Town | 1-1 | Bolton Wanderers | Crombie | | 7,872 | Draw |
| LC1L2 | 29/08/1989 | Bolton Wanderers | 5-1 | Rochdale | Philliskirk, Reeves, Savage, Cowdrill, Darby | | 4,637 | Win |
| D3 | 26/08/1989 | Bolton Wanderers | 0-0 | Fulham | | | 5,524 | Draw |
| LC1L1 | 22/08/1989 | Rochdale | 2-1 | Bolton Wanderers | Thompson S (pen) | | 3,464 | Loss |
| D3 | 19/08/1989 | Cardiff City | 0-2 | Bolton Wanderers | Philliskirk, Darby | | 4,376 | Win |