| Tuesday 15th September 1998 | |||
| 1st Leg | |||
| Barnsley | 3-0 | Reading | |
| Blackpool | 2-1 | Tranmere Rovers | |
| Bolton Wanderers | 3-1 | Hull City | |
| Bournemouth | 1-1 | Wolverhampton Wndrs | |
| Brentford | 2-3 | Tottenham Hotspur | |
| Bury | 3-0 | Crystal Palace | |
| Fulham | 1-1 | Southampton | |
| Halifax Town | 1-2 | Bradford City | |
| Huddersfield Town | 1-1 | Everton | |
| Ipswich Town | 2-1 | Luton Town | |
| Leyton Orient | 1-5 | Nottingham Forest | |
| Macclesfield Town | 0-3 | Birmingham City | |
| Northampton Town | 2-0 | West Ham United | |
| Portsmouth | 2-1 | Wimbledon | |
| Sheffield United | 2-1 | Grimsby Town | |
| Sunderland | 3-0 | Chester City | |
| Wednesday 16th September 1998 | |||
| 1st Leg | |||
| Bristol City | 1-1 | Crewe Alexandra | |
| Coventry City | 1-0 | Southend United | |
| Derby County | 1-1 | Manchester City | |
| Leicester City | 3-0 | Chesterfield | |
| Middlesbrough | 2-0 | Wycombe Wanderers | |
| Norwich City | 1-0 | Wigan Athletic | |
| Queens Park Rangers | 0-2 | Charlton Athletic | |
| Sheffield Wednesday | 0-1 | Cambridge United | |
| Tuesday 22nd September 1998 | |||
| 2nd Leg | |||
| Birmingham City | 6-0 | Macclesfield Town | (9-0) |
| Bradford City | 3-1 | Halifax Town | (5-2) |
| Cambridge United | 1-1 | Sheffield Wednesday | (2-1) |
| Charlton Athletic | 1-0 | Queens Park Rangers | (3-0) |
| Chester City | 0-1 | Sunderland | (0-4) |
| Chesterfield | 1-3 | Leicester City | (1-6) |
| Crewe Alexandra | 2-0 | Bristol City | (3-1) |
| Grimsby Town | 2-0 | Sheffield United | aet (3-2) |
| Hull City | 2-3 | Bolton Wanderers | (3-6) |
| Luton Town | 4-2 | Ipswich Town | aet (5-4) |
| Nottingham Forest | 0-0 | Leyton Orient | (5-1) |
| Southend United | 0-4 | Coventry City | (0-5) |
| Tranmere Rovers | 3-1 | Blackpool | (4-3) |
| West Ham United | 1-0 | Northampton Town | (1-2) |
| Wigan Athletic | 2-3 | Norwich City | (2-4) |
| Wimbledon | 4-1 | Portsmouth | aet (5-3) |
| Wolverhampton Wndrs | 1-2 | Bournemouth | (2-3) |
| Wycombe Wanderers | 1-1 | Middlesbrough | (1-3) |
| Wednesday 23rd September 1998 | |||
| 2nd Leg | |||
| Crystal Palace | 2-1 | Bury | (2-4) |
| Everton | 2-1 | Huddersfield Town | (3-2) |
| Manchester City | 0-1 | Derby County | (1-2) |
| Reading | 1-1 | Barnsley | (1-4) |
| Southampton | 0-1 | Fulham | (1-2) |
| Tottenham Hotspur | 3-2 | Brentford | (6-4) |
