| 2nd Round 2nd Leg |
| Tuesday, 22nd September 1998 |
| Birmingham City (LD1) | 6 | Macclesfield Town (LD2) | 0 | 3,443 |
| Birmingham City won 9-0 on aggregate |
| Bradford City (LD1) | 3 | Halifax Town (LD3) | 1 | 6,237 |
| Bradford City won 5-2 on aggregate |
| Cambridge United (LD3) | 1 | Sheffield Wednesday (PREM) | 1 | 8,502 |
| Cambridge United won 2-1 on aggregate |
| Charlton Athletic (PREM) | 1 | Queens Park Rangers (LD1) | 0 | 11,726 |
| Charlton Athletic won 3-0 on aggregate |
| Chester City (LD3) | 0 | Sunderland (LD1) | 1 | 2,738 |
| Sunderland won 4-0 on aggregate |
| Chesterfield (LD2) | 1 | Leicester City (PREM) | 3 | 4,565 |
| Leicester City won 6-1 on aggregate |
| Crewe Alexandra (LD1) | 2 | Bristol City (LD1) | 0 | 3,089 |
| Crewe Alexandra won 3-1 on aggregate |
| Grimsby Town (LD1) | 2 | Sheffield United (LD1) | 0 | 4,287 |
| after extra time, 90 minutes 1-0, Grimsby Town won 3-2 on aggregate |
| Hull City (LD3) | 2 | Bolton Wanderers (LD1) | 3 | 4,226 |
| Bolton Wanderers won 6-3 on aggregate |
| Luton Town (LD2) | 4 | Ipswich Town (LD1) | 2 | 5,665 |
| after extra time, 90 minutes 2-1, Luton Town won 5-4 on aggregate |
| Nottingham Forest (PREM) | 0 | Leyton Orient (LD3) | 0 | 6,382 |
| Nottingham Forest won 5-1 on aggregate |
| Southend United (LD3) | 0 | Coventry City (PREM) | 4 | 6,292 |
| Coventry City won 5-0 on aggregate |
| Tranmere Rovers (LD1) | 3 | Blackpool (LD2) | 1 | 5,765 |
| Tranmere Rovers won 4-3 on aggregate |
| West Ham United (PREM) | 1 | Northampton Town (LD2) | 0 | 25,435 |
| Northampton Town won 2-1 on aggregate |
| Wigan Athletic (LD2) | 2 | Norwich City (LD1) | 3 | 3,402 |
| Norwich City won 4-2 on aggregate |
| Wimbledon (PREM) | 4 | Portsmouth (LD1) | 1 | 3,756 |
| after extra time, 90 minutes 2-1, Wimbledon won 5-3 on aggregate |
| Wolverhampton Wanderers (LD1) | 1 | Bournemouth (LD2) | 2 | 15,431 |
| Bournemouth won 3-2 on aggregate |
| Wycombe Wanderers (LD2) | 1 | Middlesbrough (PREM) | 1 | 5,698 |
| Middlesbrough won 3-1 on aggregate |
| Wednesday, 23rd September 1998 |
| Crystal Palace (LD1) | 2 | Bury (LD1) | 1 | 3,546 |
| Bury won 4-2 on aggregate |
| Everton (PREM) | 2 | Huddersfield Town (LD1) | 1 | 18,718 |
| Everton won 3-2 on aggregate |
| Manchester City (LD2) | 0 | Derby County (PREM) | 1 | 19,622 |
| Derby County won 2-1 on aggregate |
| Reading (LD2) | 1 | Barnsley (LD1) | 1 | 6,983 |
| Barnsley won 4-1 on aggregate |
| Southampton (PREM) | 0 | Fulham (LD2) | 1 | 11,645 |
| Fulham won 2-1 on aggregate |
| Tottenham Hotspur (PREM) | 3 | Brentford (LD3) | 2 | 22,980 |
| Tottenham Hotspur won 6-4 on aggregate |
| 1st Round 2nd Leg |
| Tuesday, 18th August 1998 |
| Barnsley (LD1) | 3 | Scarborough (LD3) | 0 | 7,978 |
| Barnsley won 4-0 on aggregate |
| Brentford (LD3) | 3 | West Bromwich Albion (LD1) | 0 | 4,664 |
| Brentford won 4-2 on aggregate |
| Bristol Rovers (LD2) | 1 | Leyton Orient (LD3) | 2 | 4,235 |
| after extra time, 90 minutes 1-1, Leyton Orient won 3-2 on aggregate |
| Burnley (LD2) | 1 | Bury (LD1) | 4 | 5,453 |
| Bury won 5-2 on aggregate |
| Cardiff City (LD3) | 1 | Fulham (LD2) | 2 | 4,768 |
| Fulham won 4-2 on aggregate |
| Carlisle United (LD3) | 0 | Tranmere Rovers (LD1) | 1 | 2,106 |
| Tranmere Rovers won 4-0 on aggregate |
| Chester City (LD3) | 2 | Port Vale (LD1) | 2 | 2,461 |
| Chester City won 4-3 on aggregate |
| Chesterfield (LD2) | 2 | Rotherham United (LD3) | 0 | 3,487 |
| Chesterfield won 3-0 on aggregate |
| Colchester United (LD2) | 3 | Bournemouth (LD2) | 2 | 2,550 |
| Bournemouth won 4-3 on aggregate |
| Crewe Alexandra (LD1) | 2 | Oldham Athletic (LD2) | 0 | 3,428 |
| Crewe Alexandra won 4-3 on aggregate |
| Darlington (LD3) | 2 | Sheffield United (LD1) | 2 | 3,756 |
| after extra time, 90 minutes 2-0, Sheffield United won 5-3 on aggregate |
| Gillingham (LD2) | 0 | Southend United (LD3) | 1 | 3,417 |
| Southend United won 2-0 on aggregate |
| Halifax Town (LD3) | 0 | Wrexham (LD2) | 2 | 2,692 |
| after extra time, 90 minutes 0-2, aggregate 2-2, Wrexham won 3-2 on penalties |
| Hartlepool United (LD3) | 0 | Bolton Wanderers (LD1) | 3 | 3,185 |
| Bolton Wanderers won 4-0 on aggregate |
| Hull City (LD3) | 0 | Stockport County (LD1) | 0 | 3,480 |
| after extra time, 90 minutes 0-0, aggregate 2-2, Hull City won on away goals rule |
| Ipswich Town (LD1) | 5 | Exeter City (LD3) | 1 | 7,952 |
| Ipswich Town won 6-2 on aggregate |
| Lincoln City (LD2) | 0 | Bradford City (LD1) | 1 | 3,066 |
| Bradford City won 2-1 on aggregate |
| Mansfield Town (LD3) | 1 | Huddersfield Town (LD1) | 1 | 2,936 |
| Huddersfield Town won 4-3 on aggregate |
| Millwall (LD2) | 1 | Birmingham City (LD1) | 1 | 4,478 |
| Birmingham City won 3-1 on aggregate |
| Norwich City (LD1) | 1 | Swansea City (LD3) | 0 | 13,146 |
| after extra time, 90 minutes 0-0, Norwich City won 2-1 on aggregate |
| Oxford United (LD1) | 1 | Luton Town (LD2) | 3 | 5,099 |
| Luton Town won 5-4 on aggregate |
| Portsmouth (LD1) | 3 | Plymouth Argyle (LD3) | 2 | 5,479 |
| Portsmouth won 6-3 on aggregate |
| Preston North End (LD2) | 0 | Grimsby Town (LD1) | 0 | 5,650 |
| after extra time, 90 minutes 0-0, aggregate 0-0, Grimsby Town won 7-6 on penalties |
| Rochdale (LD3) | 0 | Wigan Athletic (LD2) | 1 | 1,697 |
| Wigan Athletic won 2-0 on aggregate |
| Scunthorpe United (LD3) | 1 | Blackpool (LD2) | 1 | 2,211 |
| Blackpool won 2-1 on aggregate |
| Shrewsbury Town (LD3) | 4 | Bristol City (LD1) | 3 | 1,011 |
| Bristol City won 7-4 on aggregate |
| Sunderland (LD1) | 2 | York City (LD2) | 1 | 22,695 |
| Sunderland won 4-1 on aggregate |
| Watford (LD1) | 1 | Cambridge United (LD3) | 1 | 6,817 |
| Cambridge United won 2-1 on aggregate |
| Wolverhampton Wanderers (LD1) | 5 | Barnet (LD3) | 0 | 15,296 |
| Wolverhampton Wanderers won 6-2 on aggregate |
| Wycombe Wanderers (LD2) | 2 | Swindon Town (LD1) | 0 | 2,478 |
| Wycombe Wanderers won 3-2 on aggregate |
| Wednesday, 19th August 1998 |
| Brighton & Hove Albion (LD3) | 1 | Northampton Town (LD2) | 1 | 1,291 |
| after extra time, 90 minutes 1-0, Northampton Town won 3-2 on aggregate |
| Manchester City (LD2) | 7 | Notts. County (LD2) | 1 | 10,063 |
| Manchester City won 9-1 on aggregate |
| Stoke City (LD2) | 1 | Macclesfield Town (LD2) | 0 | 6,152 |
| Macclesfield Town won 3-2 on aggregate |
| Tuesday, 25th August 1998 |
| Crystal Palace (LD1) | 2 | Torquay United (LD3) | 1 | 6,872 |
| after extra time, 90 minutes 1-1, Crystal Palace won 3-2 on aggregate |
| Wednesday, 26th August 1998 |
| Queens Park Rangers (LD1) | 3 | Walsall (LD2) | 1 | 5,052 |
| after extra time, 90 minutes 1-1, Queens Park Rangers won 3-1 on aggregate |
| Reading (LD2) | 2 | Peterborough United (LD3) | 0 | 9,151 |
| Reading won 3-1 on aggregate |
