| D1PF | 31/05/1999 | Bolton Wanderers | 0-2 | Watford | (played at Wembley Stadium) | Highlights | 70,343 | Loss |
| D1PSFL2 | 19/05/1999 | Ipswich Town | 4-3 | Bolton Wanderers | Taylor B 2, Frandsen (aet) | Highlights | 21,755 | Loss |
| D1PSFL1 | 16/05/1999 | Bolton Wanderers | 1-0 | Ipswich Town | Johansen | | 18,295 | Win |
| D1 | 09/05/1999 | Portsmouth | 0-2 | Bolton Wanderers | Johansen, Gudjohnsen | | 16,015 | Win |
| D1 | 05/05/1999 | Bolton Wanderers | 1-2 | Stockport County | Taylor B | | 18,587 | Loss |
| D1 | 30/04/1999 | Bolton Wanderers | 1-1 | Wolverhampton Wanderers | Gardner | Highlights | 20,208 | Draw |
| D1 | 23/04/1999 | Bury | 2-1 | Bolton Wanderers | Cox | | 7,680 | Loss |
| D1 | 20/04/1999 | Norwich City | 2-2 | Bolton Wanderers | Cox, Frandsen | | 11,137 | Draw |
| D1 | 17/04/1999 | Bolton Wanderers | 2-0 | Ipswich Town | Taylor B, Gudjohnsen | | 19,894 | Win |
| D1 | 13/04/1999 | Bolton Wanderers | 1-0 | Bristol City | Gudjohnsen | | 14,459 | Win |
| D1 | 10/04/1999 | Watford | 2-0 | Bolton Wanderers | | | 13,001 | Loss |
| D1 | 03/04/1999 | Oxford United | 0-0 | Bolton Wanderers | | Highlights | 7,547 | Draw |
| D1 | 20/03/1999 | Sunderland | 3-1 | Bolton Wanderers | Frandsen | Highlights | 41,505 | Loss |
| D1 | 13/03/1999 | Bolton Wanderers | 2-1 | Queens Park Rangers | Taylor B 2 | | 17,919 | Win |
| D1 | 09/03/1999 | Bolton Wanderers | 3-3 | Barnsley | Sellars, Holdsworth (pen), Gudjohnsen | | 16,537 | Draw |
| D1 | 06/03/1999 | Swindon Town | 3-3 | Bolton Wanderers | Fish, Jensen, Gudjohnsen | | 8,392 | Draw |
| D1 | 02/03/1999 | Huddersfield Town | 3-2 | Bolton Wanderers | Holdsworth, Johansen | | 13,687 | Loss |
| D1 | 27/02/1999 | Bolton Wanderers | 1-3 | Crewe Alexandra | Holdsworth (pen) | | 19,437 | Loss |
| D1 | 21/02/1999 | Birmingham City | 0-0 | Bolton Wanderers | | | 26,051 | Draw |
| D1 | 13/02/1999 | Bolton Wanderers | 2-1 | West Bromwich Albion | Taylor B, Cox | | 20,657 | Win |
| D1 | 06/02/1999 | Grimsby Town | 0-1 | Bolton Wanderers | Holdsworth | Highlights | 8,674 | Win |
| D1 | 30/01/1999 | Bolton Wanderers | 2-0 | Norwich City | Holdsworth, Cox | | 17,269 | Win |
| D1 | 16/01/1999 | Sheffield United | 1-2 | Bolton Wanderers | Holdsworth 2 | | 15,787 | Win |
| D1 | 10/01/1999 | Bolton Wanderers | 3-0 | Crystal Palace | Taylor B, Johansen, Jensen | Highlights | 15,410 | Win |
| FAC3 | 02/01/1999 | Bolton Wanderers | 1-2 | Wolverhampton Wanderers | Sellars | | 18,269 | Loss |
| D1 | 28/12/1998 | Port Vale | 0-2 | Bolton Wanderers | Sellars, Holdsworth (pen) | | 8,201 | Win |
| D1 | 26/12/1998 | Bolton Wanderers | 0-0 | Bradford City | | | 24,625 | Draw |
| D1 | 19/12/1998 | Bolton Wanderers | 3-1 | Portsmouth | Taylor B, Frandsen, Holdsworth | | 15,981 | Win |
| D1 | 12/12/1998 | Tranmere Rovers | 1-1 | Bolton Wanderers | Taylor B | | 6,959 | Draw |
| D1 | 05/12/1998 | Wolverhampton Wanderers | 1-1 | Bolton Wanderers | Taylor B | | 22,537 | Draw |
| D1 | 28/11/1998 | Bolton Wanderers | 4-0 | Bury | Johansen 2, Gunnlaugsson 2 | | 21,028 | Win |
| D1 | 24/11/1998 | Stockport County | 0-1 | Bolton Wanderers | Taylor B | | 8,520 | Win |
| D1 | 21/11/1998 | Ipswich Town | 0-1 | Bolton Wanderers | Taylor B | | 17,225 | Win |
| D1 | 14/11/1998 | Bolton Wanderers | 2-2 | Tranmere Rovers | Johansen, Holdsworth (pen) | | 16,564 | Draw |
| LC4 | 10/11/1998 | Bolton Wanderers | 1-2 | Wimbledon | Jensen | | 7,868 | Loss |
| D1 | 07/11/1998 | Queens Park Rangers | 2-0 | Bolton Wanderers | | | 11,814 | Loss |
| D1 | 04/11/1998 | Bolton Wanderers | 3-1 | Port Vale | Taylor B, Frandsen, Gunnlaugsson | | 13,324 | Win |
| D1 | 01/11/1998 | Bolton Wanderers | 0-3 | Sunderland | | | 21,676 | Loss |
| LC3 | 27/10/1998 | Norwich City | 1-1 | Bolton Wanderers | Elliott R (aet) (Won 3-1 on penalties) | | 14,189 | Draw |
| D1 | 23/10/1998 | Bristol City | 2-1 | Bolton Wanderers | Gunnlaugsson | | 12,026 | Loss |
| D1 | 20/10/1998 | Bolton Wanderers | 1-2 | Watford | Gunnlaugsson | | 15,921 | Loss |
| D1 | 17/10/1998 | Bolton Wanderers | 1-1 | Oxford United | Frandsen | | 17,064 | Draw |
| D1 | 03/10/1998 | Barnsley | 2-2 | Bolton Wanderers | Gunnlaugsson, Johansen | | 17,362 | Draw |
| D1 | 29/09/1998 | Bolton Wanderers | 2-1 | Swindon Town | Blake, Gunnlaugsson | | 16,497 | Win |
| D1 | 26/09/1998 | Bolton Wanderers | 3-0 | Huddersfield Town | Frandsen, Blake, Gunnlaugsson | | 20,971 | Win |
| LC2L2 | 22/09/1998 | Hull City | 2-3 | Bolton Wanderers | Jensen, Johansen, Gardner | | 4,226 | Win |
| D1 | 19/09/1998 | Crewe Alexandra | 4-4 | Bolton Wanderers | Gunnlaugsson 2, Taylor B, Frandsen | | 5,744 | Draw |
| LC2L1 | 15/09/1998 | Bolton Wanderers | 3-1 | Hull City | Phillips J, Gunnlaugsson, Frandsen | | 7,544 | Win |
| D1 | 12/09/1998 | Bolton Wanderers | 3-1 | Birmingham City | Taylor B 2, Frandsen | | 19,637 | Win |
| D1 | 08/09/1998 | West Bromwich Albion | 2-3 | Bolton Wanderers | Gunnlaugsson, Blake, Gardner | | 15,789 | Win |
| D1 | 29/08/1998 | Bolton Wanderers | 2-2 | Sheffield United | Strong, Blake | | 18,263 | Draw |
| LC1L2 | 25/08/1998 | Hartlepool United | 0-3 | Bolton Wanderers | Blake 3 | | 3,185 | Win |
| D1 | 23/08/1998 | Bradford City | 2-2 | Bolton Wanderers | Gunnlaugsson, Blake | Highlights | 13,163 | Draw |
| D1 | 15/08/1998 | Bolton Wanderers | 2-0 | Grimsby Town | Blake, Holdsworth (pen) | | 16,584 | Win |
| LC1L1 | 11/08/1998 | Bolton Wanderers | 1-0 | Hartlepool United | Taylor B | | 6,429 | Win |
| D1 | 08/08/1998 | Crystal Palace | 2-2 | Bolton Wanderers | Holdsworth, Gunnlaugsson | | 19,029 | Draw |