| 7-Aug-99 | Carlisle United | Away | League | 1-2 | Inglethorpe | 3895 | |
| 10-Aug-99 | Swindon Town | Away | LC r1-1 | 1-0 | Inglethorpe | 3587 | |
| 14-Aug-99 | Brighton & Hove Albion | Home | League | 1-2 | Richards | 7200 | |
| 21-Aug-99 | Peterborough United | Away | League | 1-2 | Lockwood | 6448 | |
| 24-Aug-99 | Swindon Town | Home | LC r1-2 | 1-1 | Lockwood | 2750 | |
| 28-Aug-99 | Halifax Town | Home | League | 1-0 | Simba | 3703 | |
| 30-Aug-99 | Southend United | Away | League | 1-1 | Walschaerts | 5991 | |
| 3-Sep-99 | Shrewsbury Town | Home | League | 1-2 | Inglethorpe | 3742 | |
| 11-Sep-99 | Mansfield Town | Away | League | 1-1 | Simba | 2491 | |
| 14-Sep-99 | Grimsby Town | Away | LC r2-1 | 1-4 | Lockwood (pen) | 2238 | |
| 18-Sep-99 | Torquay United | Home | League | 0-2 | | 4452 | |
| 21-Sep-99 | Grimsby Town | Home | LC r2-2 | 1-0 | Watts | 1036 | |
| 25-Sep-99 | Hartlepool United | Home | League | 2-1 | Low, Smith | 3889 | |
| 2-Oct-99 | Plymouth Argyle | Away | League | 0-5 | | 3782 | |
| 9-Oct-99 | York City | Away | League | 1-2 | Clark | 2320 | |
| 16-Oct-99 | Lincoln City | Home | League | 2-3 | Lockwood (pen), Simba | 4349 | |
| 19-Oct-99 | Barnet | Home | League | 0-0 | | 3497 | |
| 23-Oct-99 | Hartlepool United | Away | League | 0-1 | | 2397 | |
| 30-Oct-99 | Cardiff City | Home | FAC r1 | 1-1 | Ampadu | 3109 | |
| 2-Nov-99 | Darlington | Away | League | 1-3 | Brkovic | 4542 | |
| 6-Nov-99 | Northampton Town | Home | League | 0-0 | | 3928 | |
| 9-Nov-99 | Cardiff City | Away | FAC r1r | 1-3 | Smith | 3095 | |
| 12-Nov-99 | Rotherham United | Away | League | 1-0 | Ling | 4280 | |
| 23-Nov-99 | Rochdale | Home | League | 0-0 | | 2990 | |
| 27-Nov-99 | Cheltenham Town | Away | League | 0-2 | | 3599 | |
| 4-Dec-99 | Carlisle United | Home | League | 0-1 | | 3871 | |
| 8-Dec-99 | Reading | Away | AWS s.r1 | 0-1 | | 1561 | |
| 18-Dec-99 | Macclesfield Town | Away | League | 0-1 | | 2303 | |
| 26-Dec-99 | Swansea City | Home | League | 0-1 | | 4447 | |
| 28-Dec-99 | Chester City | Away | League | 5-1 | Watts, Griffiths (3, 2 pens), Christie | 2825 | |
| 3-Jan-00 | Hull City | Home | League | 0-0 | | 5169 | |
| 8-Jan-00 | Exeter City | Away | League | 3-1 | Watts, Smith, Christie | 2434 | |
| 15-Jan-00 | Brighton & Hove Albion | Away | League | 1-0 | Brkovic | 5902 | |
| 22-Jan-00 | Peterborough United | Home | League | 1-1 | Brkovic | 4795 | |
| 29-Jan-00 | Halifax Town | Away | League | 2-0 | Watts, Christie | 2655 | |
| 5-Feb-00 | Southend United | Home | League | 2-1 | Watts, Brkovic | 5972 | |
| 8-Feb-00 | Exeter City | Home | League | 4-1 | Walschaerts, Watts, Lockwood, Richards | 3854 | |
| 12-Feb-00 | Shrewsbury Town | Away | League | 0-1 | | 2740 | |
| 19-Feb-00 | Cheltenham Town | Home | League | 1-0 | Walchaerts | 4884 | |
| 26-Feb-00 | Torquay United | Away | League | 0-0 | | 2470 | |
| 4-Mar-00 | Mansfield Town | Home | League | 1-3 | Smith | 4281 | |
| 7-Mar-00 | Northampton Town | Away | League | 1-2 | Christie | 5121 | |
| 11-Mar-00 | Darlington | Home | League | 2-1 | Lockwood, Watts | 4053 | |
| 18-Mar-00 | Rochdale | Away | League | 4-1 | Christie (2), Smith, Lockwood | 2472 | |
| 21-Mar-00 | Rotherham United | Home | League | 0-1 | | 3959 | |
| 25-Mar-00 | Swansea City | Away | League | 0-0 | | 5330 | |
| 1-Apr-00 | Macclesfield Town | Home | League | 0-0 | | 4302 | |
| 8-Apr-00 | Hull City | Away | League | 0-2 | | 4422 | |
| 15-Apr-00 | Chester City | Home | League | 1-2 | Griffiths | 4123 | |
| 22-Apr-00 | Lincoln City | Away | League | 0-0 | | 2718 | |
| 24-Apr-00 | Plymouth Argyle | Home | League | 3-0 | McGhee, Brkovic, Christie | 4113 | |
| 29-Apr-00 | Barnet | Away | League | 2-2 | Lockwood (pen), Beall | 4030 | |
| 6-May-00 | York City | Home | League | 0-0 | | 4594 | |
