| 2nd Round 2nd Leg |
| Tuesday, 21st September 1999 |
| Aston Villa (PREM) | 5 | Chester City (LD3) | 0 | 22,613 |
| Aston Villa won 6-0 on aggregate |
| Bolton Wanderers (LD1) | 2 | Gillingham (LD2) | 0 | 3,673 |
| Bolton Wanderers won 6-1 on aggregate |
| Bournemouth (LD2) | 0 | Charlton Athletic (LD1) | 0 | 4,369 |
| after extra time, 90 minutes 0-0, aggregate 0-0, Bournemouth won 3-1 on penalties |
| Bristol Rovers (LD2) | 0 | Birmingham City (LD1) | 1 | 5,456 |
| Birmingham City won 3-0 on aggregate |
| Fulham (LD1) | 2 | Norwich City (LD1) | 0 | 5,246 |
| Fulham won 6-0 on aggregate |
| Ipswich Town (LD1) | 1 | Crewe Alexandra (LD1) | 1 | 9,689 |
| Crewe Alexandra won 3-2 on aggregate |
| Leyton Orient (LD3) | 1 | Grimsby Town (LD1) | 0 | 1,036 |
| Grimsby Town won 4-2 on aggregate |
| Liverpool (PREM) | 4 | Hull City (LD3) | 2 | 24,318 |
| Liverpool won 9-3 on aggregate |
| Middlesbrough (PREM) | 2 | Chesterfield (LD2) | 1 | 25,602 |
| Middlesbrough won 2-1 on aggregate |
| Notts. County (LD2) | 2 | Huddersfield Town (LD1) | 2 | 4,104 |
| Huddersfield Town won 4-3 on aggregate |
| Preston North End (LD2) | 3 | Sheffield United (LD1) | 0 | 5,658 |
| Preston North End won 3-2 on aggregate |
| Southampton (PREM) | 4 | Manchester City (LD1) | 3 | 10,960 |
| after extra time, 90 minutes 3-3, Southampton won 4-3 on aggregate |
| Stockport County (LD1) | 3 | Barnsley (LD1) | 3 | 3,332 |
| after extra time, 90 minutes 2-2, aggregate 4-4, Barnsley won on away goals rule |
| Walsall (LD1) | 0 | Sunderland (PREM) | 5 | 5,109 |
| Sunderland won 8-2 on aggregate |
| Wigan Athletic (LD2) | 3 | Watford (PREM) | 1 | 5,006 |
| after extra time, 90 minutes 3-1, aggregate 3-3, Watford won on away goals rule |
| Wimbledon (PREM) | 3 | Cardiff City (LD2) | 1 | 2,772 |
| Wimbledon won 4-2 on aggregate |
| Wycombe Wanderers (LD2) | 3 | West Bromwich Albion (LD1) | 4 | 5,047 |
| after extra time, 90 minutes 2-2, West Bromwich Albion won 5-4 on aggregate |
| Wednesday, 22nd September 1999 |
| Blackburn Rovers (LD1) | 3 | Portsmouth (LD1) | 1 | 7,512 |
| Blackburn Rovers won 6-1 on aggregate |
| Bristol City (LD2) | 0 | Nottingham Forest (LD1) | 0 | 8,259 |
| Nottingham Forest won 2-1 on aggregate |
| Coventry City (PREM) | 3 | Tranmere Rovers (LD1) | 1 | 12,433 |
| Tranmere Rovers won 6-4 on aggregate |
| Derby County (PREM) | 3 | Swansea City (LD3) | 1 | 19,152 |
| Derby County won 3-1 on aggregate |
| Everton (PREM) | 0 | Oxford United (LD2) | 1 | 10,006 |
| Oxford United won 2-1 on aggregate |
| Leicester City (PREM) | 4 | Crystal Palace (LD1) | 2 | 12,762 |
| Leicester City won 7-5 on aggregate |
| Reading (LD2) | 2 | Bradford City (PREM) | 2 | 6,892 |
| after extra time, 90 minutes 1-1, aggregate 3-3, Bradford City won on away goals rule |
| Sheffield Wednesday (PREM) | 3 | Stoke City (LD2) | 1 | 10,993 |
| Sheffield Wednesday won 3-1 on aggregate |
| 1st Round 2nd Leg |
| Tuesday, 24th August 1999 |
| Barnet (LD3) | 3 | Bournemouth (LD2) | 2 | 1,697 |
| Bournemouth won 4-3 on aggregate |
| Barnsley (LD1) | 2 | Lincoln City (LD3) | 2 | 7,047 |
| Barnsley won 6-4 on aggregate |
| Bolton Wanderers (LD1) | 5 | Darlington (LD3) | 3 | 4,991 |
| Bolton Wanderers won 6-4 on aggregate |
| Bristol City (LD2) | 2 | Cambridge United (LD2) | 1 | 5,352 |
| Bristol City won 4-3 on aggregate |
| Burnley (LD2) | 0 | Manchester City (LD1) | 1 | 3,647 |
| Manchester City won 6-0 on aggregate |
| Cheltenham Town (LD3) | 2 | Norwich City (LD1) | 1 | 4,203 |
| after extra time, 90 minutes 2-0, Norwich City won 3-2 on aggregate |
| Chesterfield (LD2) | 2 | Rochdale (LD3) | 1 | 2,067 |
| Chesterfield won 4-2 on aggregate |
| Crewe Alexandra (LD1) | 1 | Hartlepool United (LD3) | 0 | 5,095 |
| Crewe Alexandra won 4-3 on aggregate |
| Crystal Palace (LD1) | 3 | Colchester United (LD2) | 1 | 5,471 |
| Crystal Palace won 5-3 on aggregate |
| Exeter City (LD3) | 1 | Birmingham City (LD1) | 2 | 2,338 |
| Birmingham City won 5-1 on aggregate |
| Fulham (LD1) | 3 | Northampton Town (LD3) | 1 | 5,515 |
| Fulham won 5-2 on aggregate |
| Gillingham (LD2) | 2 | Brighton & Hove Albion (LD3) | 0 | 4,592 |
| Gillingham won 4-0 on aggregate |
| Grimsby Town (LD1) | 6 | Carlisle United (LD3) | 0 | 2,696 |
| Grimsby Town won 6-0 on aggregate |
| Huddersfield Town (LD1) | 0 | Scunthorpe United (LD2) | 0 | 4,345 |
| Huddersfield Town won 2-0 on aggregate |
| Hull City (LD3) | 2 | Rotherham United (LD3) | 0 | 4,373 |
| Hull City won 3-0 on aggregate |
| Ipswich Town (LD1) | 2 | Brentford (LD2) | 0 | 9,748 |
| Ipswich Town won 4-0 on aggregate |
| Leyton Orient (LD3) | 1 | Swindon Town (LD1) | 1 | 4,000 |
| Leyton Orient won 2-1 on aggregate |
| Mansfield Town (LD3) | 1 | Nottingham Forest (LD1) | 0 | 3,072 |
| Nottingham Forest won 3-1 on aggregate |
| Millwall (LD2) | 1 | Swansea City (LD3) | 1 | 4,542 |
| Swansea City won 3-1 on aggregate |
| Notts. County (LD2) | 2 | Bury (LD2) | 0 | 2,494 |
| Notts. County won 2-1 on aggregate |
| Oldham Athletic (LD2) | 1 | Stockport County (LD1) | 1 | 2,750 |
| Stockport County won 3-1 on aggregate |
| Oxford United (LD2) | 1 | Southend United (LD3) | 0 | 4,162 |
| Oxford United won 3-0 on aggregate |
| Peterborough United (LD3) | 1 | Reading (LD2) | 2 | 4,109 |
| Reading won 2-1 on aggregate |
| Plymouth Argyle (LD3) | 1 | Walsall (LD1) | 4 | 1,834 |
| Walsall won 8-2 on aggregate |
| Port Vale (LD1) | 4 | Chester City (LD3) | 4 | 2,625 |
| Chester City won 6-5 on aggregate |
| Portsmouth (LD1) | 3 | Torquay United (LD3) | 0 | 8,741 |
| Portsmouth won 3-0 on aggregate |
| Shrewsbury Town (LD3) | 0 | Sheffield United (LD1) | 3 | 1,723 |
| Sheffield United won 6-0 on aggregate |
| Tranmere Rovers (LD1) | 3 | Blackpool (LD2) | 1 | 4,800 |
| Tranmere Rovers won 4-3 on aggregate |
| West Bromwich Albion (LD1) | 5 | Halifax Town (LD3) | 1 | 8,316 |
| West Bromwich Albion won 5-1 on aggregate |
| Wigan Athletic (LD2) | 2 | York City (LD3) | 1 | 3,396 |
| Wigan Athletic won 3-1 on aggregate |
| Wolverhampton Wanderers (LD1) | 2 | Wycombe Wanderers (LD2) | 4 | 13,723 |
| Wycombe Wanderers won 4-3 on aggregate |
| Wrexham (LD2) | 0 | Preston North End (LD2) | 2 | 2,911 |
| Preston North End won 3-0 on aggregate |
| Wednesday, 25th August 1999 |
| Bristol Rovers (LD2) | 2 | Luton Town (LD2) | 2 | 4,414 |
| Bristol Rovers won 4-2 on aggregate |
| Queens Park Rangers (LD1) | 1 | Cardiff City (LD2) | 2 | 6,185 |
| after extra time, 90 minutes 0-1, aggregate 3-3, Cardiff City won 3-2 on penalties |
| Stoke City (LD2) | 3 | Macclesfield Town (LD3) | 0 | 5,003 |
| Stoke City won 4-1 on aggregate |
