| 27-Aug-1988 | Crewe Alexandra | Home | League | 0-0 | | 3932 | |
| 30-Aug-1988 | Aldershot | Home | LC r1-1 | 2-0 | Hull, Juryeff | 2331 | |
| 03-Sep-1988 | Stockport County | Away | League | 0-0 | | 2100 | |
| 06-Sep-1988 | Aldershot | Away | LC r1-2 | 0-0 | | 1700 | |
| 10-Sep-1988 | Hereford United | Home | League | 1-3 | Hull | 3087 | |
| 17-Sep-1988 | Hartlepool United | Away | League | 0-1 | | 1823 | |
| 20-Sep-1988 | Rotherham United | Away | League | 1-4 | Ketteridge | 4289 | |
| 23-Sep-1988 | Darlington | Home | League | 1-0 | Juryeff | 2755 | |
| 27-Sep-1988 | Stoke City | Home | LC r2-1 | 1-2 | Juryeff | 3154 | |
| 01-Oct-1988 | Torquay United | Away | League | 0-3 | | 2526 | |
| 04-Oct-1988 | York City | Home | League | 4-0 | Sitton, Comfort, Hales, Juryeff | 2487 | |
| 08-Oct-1988 | Scarborough | Away | League | 0-0 | | 2376 | |
| 11-Oct-1988 | Stoke City | Away | LC r2-2 | 2-1* | Hales (pen), Comfort | 5756 | |
| 15-Oct-1988 | Colchester United | Home | League | 8-0 | Hull (3), Sitton, Baker, Comfort, Hales (pen), Day | 3421 | |
| 22-Oct-1988 | Burnley | Away | League | 2-2 | Juryeff, Comfort | 8526 | |
| 25-Oct-1988 | Exeter City | Home | League | 4-0 | Hull, Dickenson, Comfort, Juryeff | 3873 | |
| 29-Oct-1988 | Doncaster Rovers | Away | League | 0-1 | | 2182 | |
| 01-Nov-1988 | Ipswich Town | Away | LC r3 | 0-2 | | 9751 | |
| 05-Nov-1988 | Peterborough United | Home | League | 1-2 | Juryeff | 3695 | |
| 08-Nov-1988 | Carlisle United | Home | League | 2-0 | Baker, Comfort | 2879 | |
| 12-Nov-1988 | Scunthorpe United | Away | League | 2-2 | Harvey, Juryeff | 4239 | |
| 19-Nov-1988 | Enfield | Away | FAC r1 | 1-1 | Ward | 4031 | |
| 23-Nov-1988 | Enfield | Home | FAC r1r | 2-2 | Juryeff (2) | 4826 | |
| 26-Nov-1988 | Cambridge United | Away | League | 2-2 | Juryeff, Hales | 2675 | |
| 28-Nov-1988 | Enfield | Home | FAC r1r2 | 0-1 | | 5944 | |
| 03-Dec-1988 | Lincoln City | Home | League | 3-1 | Hales, Juryeff, Ward | 3093 | |
| 06-Dec-1988 | Reading | Home | SVT s.prg7 | 1-1 | Hales (pen) | 1174 | |
| 17-Dec-1988 | Grimsby Town | Away | League | 2-2 | Juryeff, Comfort | 3446 | |
| 26-Dec-1988 | Tranmere Rovers | Home | League | 2-0 | Howard, O’Shea | 4249 | |
| 31-Dec-1988 | Wrexham | Home | League | 0-1 | | 4025 | |
| 02-Jan-1989 | Rochdale | Away | League | 3-0 | Harvey (2), Juryeff | 2036 | |
| 10-Jan-1989 | Aldershot | Away | SVT s.prg7 | 3-1 | O’Shea, Ward, Jones | 1310 | |
| 14-Jan-1989 | Stockport County | Home | League | 1-2 | Howard | 3828 | |
| 17-Jan-1989 | Colchester United | Away | SVT s.r1 | 1-3 | Hull | 1736 | |
| 21-Jan-1989 | Crewe Alexandra | Away | League | 1-2 | Campbell | 2933 | |
| 04-Feb-1989 | Rotherham United | Home | League | 3-1 | Campbell (2), Comfort | 3290 | |
| 11-Feb-1989 | Darlington | Away | League | 3-1 | Comfort, Howard, Cooper | 1833 | |
| 14-Feb-1989 | Halifax Town | Away | League | 2-2 | Comfort (2) | 1477 | |
| 18-Feb-1989 | Scarborough | Home | League | 2-3 | Campbell, Castle | 3877 | |
| 24-Feb-1989 | Colchester United | Away | League | 0-1 | | 4269 | |
| 01-Mar-1989 | Exeter City | Away | League | 1-1 | Campbell | 2890 | |
| 04-Mar-1989 | Burnley | Home | League | 3-0 | Comfort (2), Campbell | 3949 | |
| 11-Mar-1989 | Peterborough United | Away | League | 1-0 | Howard | 3706 | |
| 14-Mar-1989 | Doncaster Rovers | Home | League | 4-0 | Campbell, Harvey, Castle, Comfort | 2824 | |
| 18-Mar-1989 | Hereford United | Away | League | 1-1 | Comfort | 2063 | |
| 21-Mar-1989 | Hartlepool United | Home | League | 4-3 | Howard, Day, Campbell, Sitton | 3408 | |
| 25-Mar-1989 | Rochdale | Home | League | 3-0 | Comfort, Hales, Castle | 4591 | |
| 27-Mar-1989 | Tranmere Rovers | Away | League | 0-3 | | 6872 | |
| 01-Apr-1989 | Grimsby Town | Home | League | 5-0 | Harvey (2), Agnew (og), Comfort, Campbell | 4149 | |
| 04-Apr-1989 | Halifax Town | Home | League | 2-0 | Hales (2, 1 pen) | 3288 | |
| 08-Apr-1989 | Wrexham | Away | League | 1-0 | Comfort | 2437 | |
| 15-Apr-1989 | Torquay United | Home | League | 3-1 | Hales, Comfort, Baker | 4642 | |
| 22-Apr-1989 | York City | Away | League | 1-1 | Sitton | 2744 | |
| 29-Apr-1989 | Cambridge United | Home | League | 1-1 | Hales (pen) | 5657 | |
| 01-May-1989 | Carlisle United | Away | League | 1-2 | Castle | 2410 | |
| 06-May-1989 | Lincoln City | Away | League | 1-0 | Castle | 3579 | |
| 13-May-1989 | Scunthorpe United | Home | League | 4-1 | Cooper (3), Castle | 6366 | |
| 21-May-1989 | Scarborough | Home | PO sf-1 | 2-0 | Cooper (2) | 9289 | |
| 24-May-1989 | Scarborough | Away | PO sf-2 | 0-1 | | 4377 | |
| 30-May-1989 | Wrexham | Away | PO fn-1 | 0-0 | | 7915 | |
| 03-Jun-1989 | Wrexham | Home | PO fn-2 | 2-1 | Harvey, Cooper | 13355 | |
| * Leyton Orient won 3-2 on Penalties |
