| D1PSFL2 | 17/05/2000 | Ipswich Town | 5-3 | Bolton Wanderers | Holdsworth 2, Johnston A (aet) | Highlights | 21,543 | Loss |
| D1PSFL1 | 14/05/2000 | Bolton Wanderers | 2-2 | Ipswich Town | Holdsworth, Gudjohnsen | Highlights | 18,814 | Draw |
| D1 | 07/05/2000 | Bolton Wanderers | 1-0 | Norwich City | Holdsworth | Highlights | 17,987 | Win |
| D1 | 03/05/2000 | Bolton Wanderers | 2-1 | Wolverhampton Wanderers | Jensen, Gudjohnsen | Highlights | 18,871 | Win |
| D1 | 29/04/2000 | Crewe Alexandra | 1-3 | Bolton Wanderers | Gudjohnsen, Holdsworth (pen), Jensen | Highlights | 8,015 | Win |
| D1 | 22/04/2000 | Huddersfield Town | 0-3 | Bolton Wanderers | Hansen 2, Whitlow | Highlights | 16,404 | Win |
| D1 | 15/04/2000 | West Bromwich Albion | 4-4 | Bolton Wanderers | Hansen, Bergsson 2, Gudjohnsen | Highlights | 12,802 | Draw |
| D1 | 08/04/2000 | Bolton Wanderers | 4-3 | Walsall | Johansen (pen), Hansen 2, Phillips J | | 11,777 | Win |
| D1 | 05/04/2000 | Manchester City | 2-0 | Bolton Wanderers | | | 32,927 | Loss |
| FACSF | 02/04/2000 | Bolton Wanderers | 0-0 | Aston Villa | (aet) (Lost 4-1 on penalties) (played at Wembley Stadium) | | 62,828 | Draw |
| D1 | 25/03/2000 | Bolton Wanderers | 2-1 | Port Vale | Gudjohnsen, Johnston A | | 12,292 | Win |
| D1 | 21/03/2000 | Bolton Wanderers | 2-0 | Sheffield United | Johnston A, O'Kane | Highlights | 11,891 | Win |
| D1 | 18/03/2000 | Grimsby Town | 0-1 | Bolton Wanderers | Bergsson | | 5,289 | Win |
| D1 | 14/03/2000 | Stockport County | 0-0 | Bolton Wanderers | | | 6,412 | Draw |
| D1 | 11/03/2000 | Bolton Wanderers | 3-1 | Fulham | Holdsworth 2 (1 pen), Gudjohnsen | Highlights | 12,761 | Win |
| D1 | 07/03/2000 | Crystal Palace | 0-0 | Bolton Wanderers | | | 15,236 | Draw |
| D1 | 04/03/2000 | Bolton Wanderers | 0-2 | Charlton Athletic | | Highlights | 13,788 | Loss |
| D1 | 26/02/2000 | Barnsley | 1-1 | Bolton Wanderers | Holdsworth (pen) | | 14,604 | Draw |
| D1 | 22/02/2000 | Bolton Wanderers | 3-0 | Portsmouth | Taylor B, Jensen, Elliott R | | 12,672 | Win |
| FACQF | 19/02/2000 | Bolton Wanderers | 1-0 | Charlton Athletic | Gudjohnsen | Highlights | 20,131 | Win |
| D1 | 12/02/2000 | Birmingham City | 2-1 | Bolton Wanderers | Johnston A | | 18,426 | Loss |
| D1 | 08/02/2000 | Port Vale | 0-1 | Bolton Wanderers | Gudjohnsen | | 5,092 | Win |
| D1 | 05/02/2000 | Bolton Wanderers | 3-1 | Blackburn Rovers | Bergsson, Johansen, Gudjohnsen | | 17,687 | Win |
| FAC5 | 29/01/2000 | Cambridge United | 1-3 | Bolton Wanderers | Taylor B 2, Gudjohnsen | | 7,523 | Win |
| LCSFL2 | 26/01/2000 | Tranmere Rovers | 3-0 | Bolton Wanderers | | Highlights | 15,834 | Loss |
| D1 | 22/01/2000 | Bolton Wanderers | 1-1 | Ipswich Town | Holdsworth | | 13,266 | Draw |
| D1 | 15/01/2000 | Queens Park Rangers | 0-1 | Bolton Wanderers | Jensen | | 11,396 | Win |
| LCSFL1 | 12/01/2000 | Bolton Wanderers | 0-1 | Tranmere Rovers | | Highlights | 13,303 | Loss |
| FAC4 | 08/01/2000 | Grimsby Town | 0-2 | Bolton Wanderers | Gudjohnsen, Hansen | | 4,270 | Win |
| D1 | 03/01/2000 | Walsall | 2-0 | Bolton Wanderers | | | 6,873 | Loss |
| D1 | 28/12/1999 | Bolton Wanderers | 1-1 | West Bromwich Albion | Jensen | | 16,269 | Draw |
| FAC3 | 21/12/1999 | Bolton Wanderers | 1-0 | Cardiff City | Gudjohnsen | | 5,734 | Win |
| D1 | 18/12/1999 | Bolton Wanderers | 0-1 | Stockport County | | | 13,285 | Loss |
| LCQF | 14/12/1999 | Bolton Wanderers | 2-1 | Wimbledon | Gudjohnsen, Johansen (pen) | | 9,463 | Win |
| D1 | 07/12/1999 | Blackburn Rovers | 3-1 | Bolton Wanderers | Elliott R | Highlights | 21,046 | Loss |
| D1 | 04/12/1999 | Bolton Wanderers | 2-3 | Tranmere Rovers | Gudjohnsen, Taylor B | | 13,534 | Loss |
| LC4 | 30/11/1999 | Bolton Wanderers | 1-0 | Sheffield Wednesday | Elliott R | | 12,543 | Win |
| D1 | 27/11/1999 | Portsmouth | 0-0 | Bolton Wanderers | | | 10,431 | Draw |
| D1 | 23/11/1999 | Fulham | 1-1 | Bolton Wanderers | Gudjohnsen | | 9,642 | Draw |
| D1 | 20/11/1999 | Bolton Wanderers | 2-0 | Grimsby Town | Hansen 2 | | 12,415 | Win |
| D1 | 14/11/1999 | Sheffield United | 1-2 | Bolton Wanderers | Farrelly, Hansen | | 10,013 | Win |
| D1 | 06/11/1999 | Bolton Wanderers | 2-0 | Crystal Palace | Gudjohnsen, Jensen | | 12,744 | Win |
| D1 | 30/10/1999 | Bolton Wanderers | 2-0 | Swindon Town | Taylor B, Hansen | Highlights | 12,486 | Win |
| D1 | 27/10/1999 | Nottingham Forest | 1-1 | Bolton Wanderers | Gudjohnsen | | 15,572 | Draw |
| D1 | 24/10/1999 | Norwich City | 2-1 | Bolton Wanderers | Gardner | | 12,468 | Loss |
| D1 | 19/10/1999 | Bolton Wanderers | 2-2 | Crewe Alexandra | Gudjohnsen, Holdsworth | | 12,676 | Draw |
| D1 | 16/10/1999 | Bolton Wanderers | 1-0 | Huddersfield Town | Gardner | | 16,603 | Win |
| LC3 | 13/10/1999 | Derby County | 1-2 | Bolton Wanderers | Fish, Johansen | | 20,242 | Win |
| D1 | 09/10/1999 | Wolverhampton Wanderers | 1-0 | Bolton Wanderers | | | 18,665 | Loss |
| D1 | 02/10/1999 | Swindon Town | 0-4 | Bolton Wanderers | Cox, Holdsworth, Gardner, Elliott R | | 6,711 | Win |
| D1 | 25/09/1999 | Bolton Wanderers | 3-2 | Nottingham Forest | Gardner, Holdsworth (pen), Cox | | 14,978 | Win |
| LC2L2 | 21/09/1999 | Bolton Wanderers | 2-0 | Gillingham | Hansen, Holdsworth | | 3,673 | Win |
| D1 | 18/09/1999 | Bolton Wanderers | 2-2 | Barnsley | Tuttle (og), Gardner | | 14,621 | Draw |
| LC2L1 | 14/09/1999 | Gillingham | 1-4 | Bolton Wanderers | Cox, Gudjohnsen 2, Bergsson | Highlights | 4,996 | Win |
| D1 | 11/09/1999 | Charlton Athletic | 2-1 | Bolton Wanderers | Johansen | | 19,028 | Loss |
| D1 | 05/09/1999 | Bolton Wanderers | 3-3 | Birmingham City | Frandsen 2, Holdsworth (pen) | | 11,668 | Draw |
| D1 | 28/08/1999 | Bolton Wanderers | 0-1 | Manchester City | | | 21,671 | Loss |
| LC1L2 | 24/08/1999 | Bolton Wanderers | 5-3 | Darlington | Gudjohnsen, Gardner, Taylor B, Frandsen, Johansen (pen) | | 4,991 | Win |
| D1 | 21/08/1999 | Ipswich Town | 1-0 | Bolton Wanderers | | | 17,696 | Loss |
| D1 | 14/08/1999 | Bolton Wanderers | 2-1 | Queens Park Rangers | Holdsworth (pen), Gudjohnsen | | 13,019 | Win |
| LC1L1 | 10/08/1999 | Darlington | 1-1 | Bolton Wanderers | Frandsen | | 5,361 | Draw |
| D1 | 07/08/1999 | Tranmere Rovers | 0-0 | Bolton Wanderers | | | 7,674 | Draw |