| D3PF | 01/06/1991 | Bolton Wanderers | 0-1 | Tranmere Rovers | (played at Wembley Stadium) | Highlights | 30,217 | Loss |
| D3PSFL2 | 22/05/1991 | Bolton Wanderers | 1-0 | Bury | Philliskirk | | 19,198 | Win |
| D3PSFL1 | 19/05/1991 | Bury | 1-1 | Bolton Wanderers | Philliskirk (pen) | | 8,000 | Draw |
| D3 | 11/05/1991 | Bolton Wanderers | 1-0 | Chester City | Cunningham | | 12,826 | Win |
| D3 | 04/05/1991 | Swansea City | 1-2 | Bolton Wanderers | Darby, Storer | | 4,713 | Win |
| D3 | 27/04/1991 | Rotherham United | 2-2 | Bolton Wanderers | Cunningham 2 | | 8,045 | Draw |
| D3 | 20/04/1991 | Bolton Wanderers | 1-0 | Leyton Orient | Reeves | | 7,926 | Win |
| D3 | 16/04/1991 | Crewe Alexandra | 1-3 | Bolton Wanderers | Philliskirk 2 (2 pens), Reeves | | 4,419 | Win |
| D3 | 13/04/1991 | Bournemouth | 1-0 | Bolton Wanderers | | | 7,156 | Loss |
| D3 | 07/04/1991 | Bolton Wanderers | 3-1 | Birmingham City | Philliskirk, Darby, Cunningham | | 11,280 | Win |
| D3 | 02/04/1991 | Cambridge United | 2-1 | Bolton Wanderers | Philliskirk | | 7,763 | Loss |
| D3 | 30/03/1991 | Bolton Wanderers | 1-0 | Southend United | Darby | | 10,666 | Win |
| D3 | 26/03/1991 | Exeter City | 2-1 | Bolton Wanderers | Reeves | | 4,009 | Loss |
| D3 | 23/03/1991 | Stoke City | 2-2 | Bolton Wanderers | Darby, Storer | | 13,869 | Draw |
| D3 | 19/03/1991 | Bolton Wanderers | 1-3 | Bury | Green | Highlights | 9,006 | Loss |
| D3 | 16/03/1991 | Bolton Wanderers | 2-1 | Wigan Athletic | Reeves, Darby | | 7,812 | Win |
| D3 | 12/03/1991 | Mansfield Town | 4-0 | Bolton Wanderers | | | 3,611 | Loss |
| D3 | 09/03/1991 | Bolton Wanderers | 3-0 | Fulham | Philliskirk 2 (1 pen), Patterson | | 7,316 | Win |
| D3 | 01/03/1991 | Tranmere Rovers | 1-1 | Bolton Wanderers | Patterson | | 10,076 | Draw |
| D3 | 23/02/1991 | Reading | 0-1 | Bolton Wanderers | Cowdrill | | 5,997 | Win |
| D3 | 16/02/1991 | Bolton Wanderers | 0-0 | Grimsby Town | | | 10,318 | Draw |
| D3 | 13/02/1991 | Bolton Wanderers | 1-0 | Exeter City | Reeves | | 5,532 | Win |
| D3 | 09/02/1991 | Bolton Wanderers | 1-1 | Huddersfield Town | Philliskirk | | 7,947 | Draw |
| D3 | 05/02/1991 | Bolton Wanderers | 1-0 | Brentford | Evans (og) | | 6,731 | Win |
| D3 | 02/02/1991 | Preston North End | 1-2 | Bolton Wanderers | Philliskirk 2 (1 pen) | | 9,844 | Win |
| FAC4 | 26/01/1991 | Manchester United | 1-0 | Bolton Wanderers | | | 43,293 | Loss |
| D3 | 19/01/1991 | Bolton Wanderers | 1-0 | Shrewsbury Town | Thompson S | | 6,164 | Win |
| D3 | 12/01/1991 | Bradford City | 1-1 | Bolton Wanderers | Philliskirk | | 8,764 | Draw |
| FAC3 | 05/01/1991 | Bolton Wanderers | 1-0 | Barrow | Philliskirk | | 11,475 | Win |
| D3 | 01/01/1991 | Bolton Wanderers | 4-1 | Bournemouth | Comstive 2, Philliskirk (pen), Darby | | 7,639 | Win |
| D3 | 29/12/1990 | Birmingham City | 1-3 | Bolton Wanderers | Philliskirk, Darby, Reeves | | 7,318 | Win |
| D3 | 26/12/1990 | Southend United | 1-1 | Bolton Wanderers | Green | | 7,539 | Draw |
| D3 | 22/12/1990 | Bolton Wanderers | 2-2 | Cambridge United | Storer, Thompson S | | 5,800 | Draw |
| AMCQ | 18/12/1990 | Blackpool | 3-0 | Bolton Wanderers | | | 2,579 | Loss |
| D3 | 15/12/1990 | Fulham | 0-1 | Bolton Wanderers | Philliskirk | | 3,466 | Win |
| FAC2 | 11/12/1990 | Chesterfield | 3-4 | Bolton Wanderers | Reeves, Philliskirk, Thompson S, Storer | | 4,836 | Win |
| D3 | 01/12/1990 | Bolton Wanderers | 2-1 | Tranmere Rovers | Green, Philliskirk | | 6,941 | Win |
| D3 | 24/11/1990 | Grimsby Town | 0-1 | Bolton Wanderers | Green | | 6,240 | Win |
| FAC1 | 17/11/1990 | Witton Albion | 1-2 | Bolton Wanderers | Darby, Comstive | | 3,790 | Win |
| D3 | 10/11/1990 | Bolton Wanderers | 3-1 | Reading | Thompson S 2 (1 pen), Reeves | | 4,648 | Win |
| AMCQ | 06/11/1990 | Bolton Wanderers | 1-0 | Tranmere Rovers | Reeves | | 3,178 | Win |
| D3 | 03/11/1990 | Chester City | 0-2 | Bolton Wanderers | Reeves, Philliskirk | | 2,553 | Win |
| D3 | 27/10/1990 | Bolton Wanderers | 1-0 | Swansea City | Philliskirk | | 4,158 | Win |
| D3 | 23/10/1990 | Bolton Wanderers | 0-0 | Rotherham United | | | 4,692 | Draw |
| D3 | 20/10/1990 | Leyton Orient | 0-1 | Bolton Wanderers | Storer | | 4,121 | Win |
| D3 | 13/10/1990 | Bury | 2-2 | Bolton Wanderers | Thompson S, Philliskirk (pen) | Highlights | 5,634 | Draw |
| LC2L2 | 09/10/1990 | Bolton Wanderers | 2-3 | Coventry City | Philliskirk 2 (1 pen) | | 5,222 | Loss |
| D3 | 06/10/1990 | Bolton Wanderers | 0-1 | Stoke City | | | 8,521 | Loss |
| D3 | 02/10/1990 | Bolton Wanderers | 1-1 | Mansfield Town | Reeves | | 3,631 | Draw |
| D3 | 28/09/1990 | Wigan Athletic | 2-1 | Bolton Wanderers | Philliskirk (pen) | | 4,366 | Loss |
| LC2L1 | 26/09/1990 | Coventry City | 4-2 | Bolton Wanderers | Philliskirk 2 | Highlights | 6,193 | Loss |
| D3 | 22/09/1990 | Brentford | 4-2 | Bolton Wanderers | Green, Reeves | | 5,077 | Loss |
| D3 | 19/09/1990 | Bolton Wanderers | 1-2 | Preston North End | Darby | | 5,844 | Loss |
| D3 | 16/09/1990 | Bolton Wanderers | 3-2 | Crewe Alexandra | Philliskirk, Green, Darby | | 4,933 | Win |
| D3 | 08/09/1990 | Huddersfield Town | 4-0 | Bolton Wanderers | | | 5,419 | Loss |
| LC1L2 | 04/09/1990 | Bolton Wanderers | 2-1 | Huddersfield Town | Stubbs, Darby | | 3,101 | Win |
| D3 | 01/09/1990 | Bolton Wanderers | 0-1 | Bradford City | | | 7,031 | Loss |
| LC1L1 | 29/08/1990 | Huddersfield Town | 0-3 | Bolton Wanderers | Darby 2, Philliskirk (pen) | | 4,444 | Win |
| D3 | 25/08/1990 | Shrewsbury Town | 0-1 | Bolton Wanderers | Storer | | 4,608 | Win |