| AMCF | 28/05/1989 | Bolton Wanderers | 4-1 | Torquay United | Julian Darby, Morrison (og), Dean Crombie, Trevor Morgan (played at Wembley Stadium) | Highlights | 46,513 | Win |
| D3 | 13/05/1989 | Northampton Town | 2-3 | Bolton Wanderers | Thomas J 2, Storer | | 3,655 | Win |
| D3 | 09/05/1989 | Bolton Wanderers | 1-1 | Wigan Athletic | Storer | | 6,166 | Draw |
| D3 | 06/05/1989 | Bolton Wanderers | 4-2 | Brentford | Thomas J 2, Darby, Savage | | 4,627 | Win |
| D3 | 01/05/1989 | Bolton Wanderers | 3-1 | Huddersfield Town | Chandler, Morgan T, Thomas J | | 5,511 | Win |
| D3 | 29/04/1989 | Bury | 0-0 | Bolton Wanderers | | | 4,393 | Draw |
| D3 | 25/04/1989 | Bolton Wanderers | 1-1 | Port Vale | Chandler | | 5,296 | Draw |
| D3 | 22/04/1989 | Bolton Wanderers | 1-0 | Aldershot | Savage | | 4,407 | Win |
| AMCNFL2 | 18/04/1989 | Blackpool | 1-1 | Bolton Wanderers | Thompson S (pen) (aet) | | 9,027 | Draw |
| D3 | 15/04/1989 | Fulham | 1-1 | Bolton Wanderers | Morgan T | | 4,950 | Draw |
| AMCNFL1 | 11/04/1989 | Bolton Wanderers | 1-0 | Blackpool | Darby | | 10,345 | Win |
| D3 | 08/04/1989 | Bolton Wanderers | 3-3 | Notts County | Thomas J, Thompson S, Morgan T | | 4,521 | Draw |
| D3 | 04/04/1989 | Gillingham | 0-1 | Bolton Wanderers | Thomas J | | 3,096 | Win |
| D3 | 01/04/1989 | Chester City | 0-0 | Bolton Wanderers | | | 3,225 | Draw |
| D3 | 27/03/1989 | Bolton Wanderers | 1-0 | Preston North End | Thompson S | | 10,281 | Win |
| D3 | 25/03/1989 | Mansfield Town | 1-1 | Bolton Wanderers | Savage | | 3,256 | Draw |
| AMCNSF | 21/03/1989 | Crewe Alexandra | 1-2 | Bolton Wanderers | Winstanley, Brown P (aet) | | 5,875 | Win |
| D3 | 18/03/1989 | Bolton Wanderers | 0-0 | Southend United | | | 3,505 | Draw |
| D3 | 14/03/1989 | Chesterfield | 1-1 | Bolton Wanderers | Thompson S | | 2,877 | Draw |
| D3 | 11/03/1989 | Bolton Wanderers | 2-0 | Bristol City | Darby 2 | | 4,423 | Win |
| D3 | 04/03/1989 | Wolverhampton Wanderers | 1-0 | Bolton Wanderers | | | 13,521 | Loss |
| AMCN2 | 21/02/1989 | Bolton Wanderers | 3-1 | Wrexham | Winstanley 2, Savage (aet) | | 3,833 | Win |
| D3 | 18/02/1989 | Blackpool | 2-0 | Bolton Wanderers | | | 5,552 | Loss |
| D3 | 11/02/1989 | Bolton Wanderers | 1-0 | Swansea City | Savage | | 4,178 | Win |
| D3 | 04/02/1989 | Sheffield United | 4-0 | Bolton Wanderers | | | 11,162 | Loss |
| D3 | 28/01/1989 | Bristol Rovers | 2-0 | Bolton Wanderers | | | 5,311 | Loss |
| D3 | 21/01/1989 | Bolton Wanderers | 1-1 | Reading | Henshaw | | 5,172 | Draw |
| AMCN1 | 17/01/1989 | Preston North End | 0-1 | Bolton Wanderers | Darby | | 5,569 | Win |
| D3 | 14/01/1989 | Cardiff City | 1-0 | Bolton Wanderers | | | 4,212 | Loss |
| D3 | 06/01/1989 | Bolton Wanderers | 2-1 | Gillingham | Stevens I, Thompson S (pen) | | 4,178 | Win |
| D3 | 02/01/1989 | Bolton Wanderers | 0-0 | Mansfield Town | | | 4,936 | Draw |
| D3 | 31/12/1988 | Notts County | 2-0 | Bolton Wanderers | | | 5,096 | Loss |
| D3 | 26/12/1988 | Preston North End | 3-1 | Bolton Wanderers | Savage | | 12,124 | Loss |
| AMCQ | 20/12/1988 | Bury | 1-0 | Bolton Wanderers | | | 2,023 | Loss |
| D3 | 17/12/1988 | Bolton Wanderers | 0-1 | Chester City | | | 4,318 | Loss |
| FAC2 | 10/12/1988 | Bolton Wanderers | 1-2 | Port Vale | Keeley | | 7,499 | Loss |
| AMCQ | 06/12/1988 | Bolton Wanderers | 1-0 | Preston North End | Thompson S (pen) | | 2,695 | Win |
| D3 | 03/12/1988 | Brentford | 3-0 | Bolton Wanderers | | | 4,600 | Loss |
| FAC1R | 28/11/1988 | Chesterfield | 2-3 | Bolton Wanderers | Stevens I, Storer, Darby | | 4,168 | Win |
| D3 | 26/11/1988 | Bolton Wanderers | 2-1 | Northampton Town | Stevens I, Brookman | | 4,446 | Win |
| FAC1 | 19/11/1988 | Bolton Wanderers | 0-0 | Chesterfield | | | 4,840 | Draw |
| D3 | 12/11/1988 | Bolton Wanderers | 2-4 | Bury | Brown P, Thompson S | | 7,897 | Loss |
| D3 | 08/11/1988 | Huddersfield Town | 0-1 | Bolton Wanderers | Morgan T | | 7,802 | Win |
| D3 | 05/11/1988 | Bristol City | 1-1 | Bolton Wanderers | Morgan T | | 8,808 | Draw |
| D3 | 29/10/1988 | Bolton Wanderers | 5-0 | Chesterfield | Brown P 2, Morgan T 2, Stevens I | | 4,783 | Win |
| D3 | 25/10/1988 | Wigan Athletic | 1-1 | Bolton Wanderers | Brookman | | 4,438 | Draw |
| D3 | 22/10/1988 | Bolton Wanderers | 1-2 | Wolverhampton Wanderers | Morgan T | | 8,174 | Loss |
| D3 | 15/10/1988 | Port Vale | 2-1 | Bolton Wanderers | Brookman | | 7,985 | Loss |
| D3 | 08/10/1988 | Bolton Wanderers | 2-2 | Blackpool | Morgan T, Thompson S (pen) | | 7,106 | Draw |
| D3 | 04/10/1988 | Swansea City | 1-0 | Bolton Wanderers | | | 3,283 | Loss |
| D3 | 01/10/1988 | Bolton Wanderers | 2-0 | Sheffield United | Thompson S 2 (1 pen) | | 9,345 | Win |
| D3 | 24/09/1988 | Aldershot | 0-3 | Bolton Wanderers | Stevens I 2, Brookman | | 2,127 | Win |
| D3 | 20/09/1988 | Bolton Wanderers | 3-2 | Fulham | Savage, Thompson S, Morgan T | | 4,289 | Win |
| D3 | 17/09/1988 | Bolton Wanderers | 1-1 | Bristol Rovers | Brown P | | 4,821 | Draw |
| D3 | 10/09/1988 | Reading | 1-1 | Bolton Wanderers | Thomas J | | 4,660 | Draw |
| LC1L2 | 07/09/1988 | Chester City | 3-1 | Bolton Wanderers | Cowdrill | | 3,784 | Loss |
| D3 | 03/09/1988 | Bolton Wanderers | 4-0 | Cardiff City | Thomas J, Henshaw, Darby 2 | | 4,831 | Win |
| LC1L1 | 30/08/1988 | Bolton Wanderers | 1-0 | Chester City | Darby | | 3,535 | Win |
| D3 | 27/08/1988 | Southend United | 2-0 | Bolton Wanderers | | | 4,075 | Loss |