| 8-Aug-98 | Chester City | Away | League | 2-0 | Richards, Harris | 2541 | |
| 11-Aug-98 | Bristol Rovers | Home | LC r1-1 | 1-1 | Richards | 2663 | |
| 15-Aug-98 | Rotherham United | Home | League | 1-4 | Smith | 4457 | |
| 18-Aug-98 | Bristol Rovers | Away | LC r1-2 | 2-1 | Warren, Inglethorpe | 4235 | |
| 22-Aug-98 | Swansea City | Away | League | 1-1 | Morrison | 4629 | |
| 29-Aug-98 | Scarborough | Home | League | 0-3 | | 3845 | |
| 1-Sep-98 | Torquay United | Away | League | 1-1 | Griffiths | 2384 | |
| 5-Sep-98 | Carlisle United | Home | League | 2-1 | Griffiths (pen), Morrison | 3730 | |
| 8-Sep-98 | Mansfield Town | Home | League | 1-1 | Clark | 3186 | |
| 12-Sep-98 | Cambridge United | Away | League | 0-1 | | 3684 | |
| 15-Sep-98 | Nottingham Forest | Home | LC r2-1 | 1-5 | Reinelt | 4906 | |
| 19-Sep-98 | Brighton & Hove Albion | Home | League | 1-0 | Smith | 5620 | |
| 22-Sep-98 | Nottingham Forest | Away | LC r2-2 | 0-0 | | 6382 | |
| 26-Sep-98 | Rochdale | Away | League | 1-2 | Smith | 1742 | |
| 3-Oct-98 | Hartlepool United | Home | League | 1-1 | Clark | 3745 | |
| 9-Oct-98 | Exeter City | Home | League | 2-0 | Inglethorpe, Simba | 3349 | |
| 17-Oct-98 | Southend United | Away | League | 2-2 | Lockwood, Inglethorpe | 6700 | |
| 20-Oct-98 | Cardiff City | Away | League | 0-0 | | 5001 | |
| 24-Oct-98 | Halifax Town | Home | League | 1-0 | Inglethorpe | 3655 | |
| 31-Oct-98 | Scunthorpe United | Home | League | 1-0 | Carl Griffiths | 3919 | |
| 7-Nov-98 | Hull City | Away | League | 1-0 | Beall | 5288 | |
| 10-Nov-98 | Shrewsbury Town | Away | League | 1-1 | Smith | 2485 | |
| 14-Nov-98 | Brighton & Hove Albion | Home | FAC r1 | 4-2 | Walschaerts, Richards (3) | 7406 | |
| 21-Nov-98 | Brentford | Home | League | 2-1 | Smith (pen), Watts | 6340 | |
| 28-Nov-98 | Plymouth Argyle | Away | League | 4-2 | Ling, Richards, Griffiths (pen), Watts | 4240 | |
| 6-Dec-98 | Kingstonian | Away | FAC r2 | 0-0 | | 3495 | |
| 8-Dec-98 | Peterborough United | Away | AWS s.r1 | 0-3 | | 1801 | |
| 12-Dec-98 | Peterborough United | Home | League | 1-2 | Smith (pen) | 4718 | |
| 15-Dec-98 | Kingstonian | Home | FAC r2r | 2-1 | Walschaerts, Simba | 3129 | |
| 19-Dec-98 | Barnet | Away | League | 2-3 | Simba, Beall | 3652 | |
| 26-Dec-98 | Swansea City | Home | League | 1-1 | Smith (pen) | 5343 | |
| 28-Dec-98 | Darlington | Away | League | 1-1 | Martin Ling | 3424 | |
| 2-Jan-99 | Southport | Away | FAC r3 | 2-0 | Smith (pen), Carl Griffiths | 4950 | |
| 9-Jan-99 | Chester City | Home | League | 2-2 | Simba (2) | 4132 | |
| 16-Jan-99 | Rotherham United | Away | League | 1-3 | Watts | 3139 | |
| 23-Jan-99 | Bristol Rovers | Away | FAC r4 | 0-3 | | 9274 | |
| 30-Jan-99 | Darlington | Home | League | 3-2 | Walschaerts, Smith, Richards | 3972 | |
| 6-Feb-99 | Carlisle United | Away | League | 1-1 | Watts | 2794 | |
| 13-Feb-99 | Mansfield Town | Away | League | 2-1 | Ling, Richards | 2817 | |
| 20-Feb-99 | Cambridge United | Home | League | 2-0 | Ling, Griffiths | 6222 | |
| 27-Feb-99 | Brighton & Hove Albion | Away | League | 2-1 | Lockwood, Griffiths (pen) | 4825 | |
| 2-Mar-99 | Torquay United | Home | League | 2-0 | Lockwood, Watts | 4099 | |
| 6-Mar-99 | Rochdale | Home | League | 3-0 | Ampadu, Griffiths (2) | 4927 | |
| 13-Mar-99 | Hull City | Home | League | 1-2 | Richards | 5481 | |
| 20-Mar-99 | Scunthorpe United | Away | League | 0-2 | | 4163 | |
| 26-Mar-99 | Halifax Town | Away | League | 2-1 | Clark, Omoyinmi | 2978 | |
| 3-Apr-99 | Southend United | Home | League | 0-3 | | 6537 | |
| 5-Apr-99 | Exeter City | Away | League | 1-1 | Walschaerts | 2764 | |
| 10-Apr-99 | Cardiff City | Home | League | 1-1 | Eckhardt (og) | 5238 | |
| 13-Apr-99 | Plymouth Argyle | Home | League | 4-3 | Richards, Morrison, Inglethorpe, Watts | 4095 | |
| 17-Apr-99 | Brentford | Away | League | 0-0 | | 8245 | |
| 21-Apr-99 | Scarborough | Away | League | 3-1 | Richards, Simba (2) | 1410 | |
| 24-Apr-99 | Shrewsbury Town | Home | League | 6-1 | Walschaerts, Smith, Clark, Simba (2), Gayle (og) | 4957 | |
| 27-Apr-99 | Hartlepool United | Away | League | 0-1 | | 3164 | |
| 1-May-99 | Peterborough United | Away | League | 0-3 | | 6189 | |
| 8-May-99 | Barnet | Home | League | 2-2 | Simba (2) | 6271 | |
| 16-May-99 | Rotherham United | Home | PO sf-1 | 0-0 | | 9419 | |
| 19-May-99 | Rotherham United | Away | PO sf-2 | 0-0* | | 9529 | |
| 29-May-99 | Scunthorpe United | Wembley Stadium | PO fn | 0-1 | | 36985 | |
| * Leyton Orient won 4-2 on Penalties | |
