| Monday 29th August 1988 | |||
| 1st Leg | |||
| Hereford United | 0-3 | Plymouth Argyle | |
| Stockport County | 0-1 | Tranmere Rovers | |
| Wigan Athletic | 0-0 | Preston North End | |
| Tuesday 30th August 1988 | |||
| 1st Leg | |||
| Bolton Wanderers | 1-0 | Chester City | |
| Bournemouth | 1-0 | Bristol Rovers | |
| Bristol City | 1-0 | Exeter City | |
| Bury | 2-1 | Wrexham | |
| Cambridge United | 1-2 | Gillingham | |
| Cardiff City | 0-1 | Swansea City | |
| Carlisle United | 1-1 | Blackpool | |
| Colchester United | 0-0 | Northampton Town | |
| Crewe Alexandra | 1-1 | Lincoln City | |
| Doncaster Rovers | 1-1 | Darlington | |
| Fulham | 2-2 | Brentford | |
| Grimsby Town | 0-1 | Rotherham United | |
| Hartlepool United | 2-2 | Sheffield United | |
| Leyton Orient | 2-0 | Aldershot | |
| Notts County | 5-0 | Mansfield Town | |
| Port Vale | 3-2 | Chesterfield | |
| Rochdale | 3-3 | Burnley | |
| Scunthorpe United | 3-2 | Huddersfield Town | |
| Shrewsbury Town | 2-2 | Walsall | |
| Southend United | 2-0 | Brighton and Hove A | |
| Torquay United | 0-1 | Reading | |
| Wolverhampton Wndrs | 3-2 | Birmingham City | |
| York City | 0-0 | Sunderland | |
| Wednesday 31st August 1988 | |||
| 1st Leg | |||
| Scarborough | 1-1 | Halifax Town | |
| West Bromwich Albion | 0-3 | Peterborough United | |
| Monday 5th September 1988 | |||
| 2nd Leg | |||
| Tranmere Rovers | 1-1 | Stockport County | (2-1) |
| Tuesday 6th September 1988 | |||
| 2nd Leg | |||
| Aldershot | 0-0 | Leyton Orient | (0-2) |
| Birmingham City | 1-0 | Wolverhampton Wndrs | aet (3-3) |
| (Birmingham City won on away goals) | |||
| Blackpool | 3-0 | Carlisle United | (4-1) |
| Brentford | 1-0 | Fulham | aet (3-2) |
| Burnley | 2-1 | Rochdale | (5-4) |
| Chesterfield | 1-1 | Port Vale | (3-4) |
| Darlington | 2-0 | Doncaster Rovers | (3-1) |
| Gillingham | 3-1 | Cambridge United | (5-2) |
| Halifax Town | 2-2 | Scarborough | aet (3-3) |
| (Scarborough won on away goals) | |||
| Huddersfield Town | 2-2 | Scunthorpe United | aet (4-5) |
| Mansfield Town | 1-0 | Notts County | (1-5) |
| Northampton Town | 5-0 | Colchester United | (5-0) |
| Plymouth Argyle | 3-2 | Hereford United | (6-2) |
| Preston North End | 1-0 | Wigan Athletic | (1-0) |
| Rotherham United | 1-0 | Grimsby Town | (2-0) |
| Sheffield United | 2-0 | Hartlepool United | aet (4-2) |
| Sunderland | 4-0 | York City | (4-0) |
| Walsall | 3-0 | Shrewsbury Town | (5-2) |
| Wrexham | 2-2 | Bury | aet (3-4) |
| Wednesday 7th September 1988 | |||
| 2nd Leg | |||
| Brighton and Hove A | 0-1 | Southend United | (0-3) |
| Bristol Rovers | 0-0 | Bournemouth | (0-1) |
| Chester City | 3-1 | Bolton Wanderers | (3-2) |
| Exeter City | 0-1 | Bristol City | (0-2) |
| Lincoln City | 2-1 | Crewe Alexandra | (3-2) |
| Peterborough United | 0-2 | West Bromwich Albion | (3-2) |
| Reading | 3-1 | Torquay United | (4-1) |
| Tuesday 20th September 1988 | |||
| 2nd Leg | |||
| Swansea City | 0-2 | Cardiff City | (1-2) |
