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| 1st(1st leg) | Hereford United | - | Plymouth Argyle | 0:3 | ||
| 2nd (2nd leg) | Plymouth Argyle | - | Hereford United | 3:2 | ||
| 1st(1st leg): 29/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Plymouth Argyle | ||||
| 1st(1st leg) | Stockport County | - | Tranmere Rovers | 0:1 | ||
| 2nd (2nd leg) | Tranmere Rovers | - | Stockport County | 1:1 | ||
| 1st(1st leg): 29/08/1988 | 2nd (2nd leg): 05/09/1988 | Winner: Tranmere Rovers | ||||
| 1st(1st leg) | Wigan Athletic | - | Preston North End | 0:0 | ||
| 2nd (2nd leg) | Preston North End | - | Wigan Athletic | 1:0 | ||
| 1st(1st leg): 29/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Preston North End | ||||
| 1st(1st leg) | AFC Bournemouth | - | Bristol Rovers | 1:0 | ||
| 2nd (2nd leg) | Bristol Rovers | - | AFC Bournemouth | 0:0 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 07/09/1988 | Winner: AFC Bournemouth | ||||
| 1st(1st leg) | Bolton Wanderers | - | Chester City | 1:0 | ||
| 2nd (2nd leg) | Chester City | - | Bolton Wanderers | 3:1 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 07/09/1988 | Winner: Chester City | ||||
| 1st(1st leg) | Bristol City | - | Exeter City | 1:0 | ||
| 2nd (2nd leg) | Exeter City | - | Bristol City | 0:1 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 07/09/1988 | Winner: Bristol City | ||||
| 1st(1st leg) | Bury FC | - | Wrexham AFC | 2:1 | ||
| 2nd (2nd leg) | Wrexham AFC | - | Bury FC | 2:2 aet | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Bury FC | ||||
| 1st(1st leg) | Cambridge United | - | Gillingham FC | 1:2 | ||
| 2nd (2nd leg) | Gillingham FC | - | Cambridge United | 3:1 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Gillingham FC | ||||
| 1st(1st leg) | Cardiff City | - | Swansea City | 0:1 | ||
| 2nd (2nd leg) | Swansea City | - | Cardiff City | 0:2 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 20/09/1988 | Winner: Cardiff City | ||||
| 1st(1st leg) | Carlisle United | - | Blackpool FC | 1:1 | ||
| 2nd (2nd leg) | Blackpool FC | - | Carlisle United | 3:0 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Blackpool FC | ||||
| 1st(1st leg) | Colchester United | - | Northampton Town | 0:0 | ||
| 2nd (2nd leg) | Northampton Town | - | Colchester United | 5:0 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Northampton Town | ||||
| 1st(1st leg) | Crewe Alexandra | - | Lincoln City | 1:1 | ||
| 2nd (2nd leg) | Lincoln City | - | Crewe Alexandra | 2:1 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 07/09/1988 | Winner: Lincoln City | ||||
| 1st(1st leg) | Doncaster Rovers | - | Darlington FC | 1:1 | ||
| 2nd (2nd leg) | Darlington FC | - | Doncaster Rovers | 2:0 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Darlington FC | ||||
| 1st(1st leg) | Fulham FC | - | Brentford FC | 2:2 | ||
| 2nd (2nd leg) | Brentford FC | - | Fulham FC | 1:0 aet | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Brentford FC | ||||
| 1st(1st leg) | Grimsby Town | - | Rotherham United | 0:1 | ||
| 2nd (2nd leg) | Rotherham United | - | Grimsby Town | 1:0 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Rotherham United | ||||
| 1st(1st leg) | Hartlepool United | - | Sheffield United | 2:2 | ||
| 2nd (2nd leg) | Sheffield United | - | Hartlepool United | 2:0 aet | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Sheffield United | ||||
| 1st(1st leg) | Leyton Orient | - | Aldershot FC | 2:0 | ||
| 2nd (2nd leg) | Aldershot FC | - | Leyton Orient | 0:0 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Leyton Orient | ||||
| 1st(1st leg) | Notts County | - | Mansfield Town | 5:0 | ||
| 2nd (2nd leg) | Mansfield Town | - | Notts County | 1:0 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Notts County | ||||
| 1st(1st leg) | Port Vale FC | - | Chesterfield FC | 3:2 | ||
| 2nd (2nd leg) | Chesterfield FC | - | Port Vale FC | 1:1 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Port Vale FC | ||||
| 1st(1st leg) | Rochdale AFC | - | Burnley FC | 3:3 | ||
| 2nd (2nd leg) | Burnley FC | - | Rochdale AFC | 2:1 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Burnley FC | ||||
| 1st(1st leg) | Scunthorpe United | - | Huddersfield Town | 3:2 | ||
| 2nd (2nd leg) | Huddersfield Town | - | Scunthorpe United | 2:2 aet | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Scunthorpe United | ||||
| 1st(1st leg) | Shrewsbury Town | - | Walsall FC | 2:2 | ||
| 2nd (2nd leg) | Walsall FC | - | Shrewsbury Town | 3:0 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Walsall FC | ||||
| 1st(1st leg) | Southend United | - | Brighton & Hove Albion | 2:0 | ||
| 2nd (2nd leg) | Brighton & Hove Albion | - | Southend United | 0:1 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 07/09/1988 | Winner: Southend United | ||||
| 1st(1st leg) | Torquay United | - | Reading FC | 0:1 | ||
| 2nd (2nd leg) | Reading FC | - | Torquay United | 3:1 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 07/09/1988 | Winner: Reading FC | ||||
| 1st(1st leg) | Wolverhampton Wanderers | - | Birmingham City | 3:2 | ||
| 2nd (2nd leg) | Birmingham City | - | Wolverhampton Wanderers | 1:0 aet | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Birmingham City | ||||
| 1st(1st leg) | York City | - | Sunderland AFC | 0:0 | ||
| 2nd (2nd leg) | Sunderland AFC | - | York City | 4:0 | ||
| 1st(1st leg): 30/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Sunderland AFC | ||||
| 1st(1st leg) | Scarborough FC | - | Halifax Town | 1:1 | ||
| 2nd (2nd leg) | Halifax Town | - | Scarborough FC | 2:2 aet | ||
| 1st(1st leg): 31/08/1988 | 2nd (2nd leg): 06/09/1988 | Winner: Scarborough FC | ||||
| 1st(1st leg) | West Bromwich Albion | - | Peterborough United | 0:3 | ||
| 2nd (2nd leg) | Peterborough United | - | West Bromwich Albion | 0:2 | ||
| 1st(1st leg): 31/08/1988 | 2nd (2nd leg): 07/09/1988 | Winner: Peterborough United | ||||
