| Monday 26th September 1988 | |||
| 1st Leg | |||
| Port Vale | 1-0 | Ipswich Town | |
| Tuesday 27th September 1988 | |||
| 1st Leg | |||
| Barnsley | 0-2 | Wimbledon | |
| Birmingham City | 0-2 | Aston Villa | |
| Blackburn Rovers | 3-1 | Brentford | |
| Blackpool | 2-0 | Sheffield Wednesday | |
| Bournemouth | 0-4 | Coventry City | |
| Darlington | 2-0 | Oldham Athletic | |
| Everton | 3-0 | Bury | |
| Leyton Orient | 1-2 | Stoke City | |
| Luton Town | 1-1 | Burnley | |
| Millwall | 3-0 | Gillingham | |
| Northampton Town | 1-1 | Charlton Athletic | |
| Notts County | 1-1 | Tottenham Hotspur | |
| Peterborough United | 1-2 | Leeds United | |
| Portsmouth | 2-2 | Scarborough | |
| Scunthorpe United | 4-1 | Chelsea | |
| Sheffield United | 3-0 | Newcastle United | |
| Sunderland | 0-3 | West Ham United | |
| Swindon Town | 1-2 | Crystal Palace | |
| Wednesday 28th September 1988 | |||
| 1st Leg | |||
| Derby County | 1-0 | Southend United | |
| Hull City | 1-2 | Arsenal | |
| Leicester City | 4-1 | Watford | |
| Lincoln City | 1-1 | Southampton | |
| Liverpool | 1-0 | Walsall | |
| Manchester City | 1-0 | Plymouth Argyle | |
| Middlesbrough | 0-0 | Tranmere Rovers | |
| Norwich City | 2-0 | Preston North End | |
| Nottingham Forest | 6-0 | Chester City | |
| Oxford United | 2-4 | Bristol City | |
| Queens Park Rangers | 3-0 | Cardiff City | |
| Reading | 1-1 | Bradford City | |
| Rotherham United | 0-1 | Manchester United | |
| Tuesday 11th October 1988 | |||
| 2nd Leg | |||
| Bristol City | 2-0 | Oxford United | (6-2) |
| Burnley | 0-1 | Luton Town | (1-2) |
| Bury | 2-2 | Everton | (2-5) |
| Cardiff City | 1-4 | Queens Park Rangers | (1-7) |
| Charlton Athletic | 2-1 | Northampton Town | (3-2) |
| Coventry City | 3-1 | Bournemouth | (7-1) |
| Gillingham | 1-3 | Millwall | (1-6) |
| Ipswich Town | 3-0 | Port Vale | (3-1) |
| Oldham Athletic | 4-0 | Darlington | aet (4-2) |
| Preston North End | 0-3 | Norwich City | (0-5) |
| Southampton | 3-1 | Lincoln City | (4-2) |
| Southend United | 1-2 | Derby County | (1-3) |
| Stoke City | 1-2 | Leyton Orient | aet (3-3) |
| (Leyton Orient won on penalties) | |||
| Tottenham Hotspur | 2-1 | Notts County | (3-2) |
| Tranmere Rovers | 1-0 | Middlesbrough | (1-0) |
| Watford | 2-2 | Leicester City | (3-6) |
| Wednesday 12th October 1988 | |||
| 2nd Leg | |||
| Arsenal | 3-0 | Hull City | (5-1) |
| Aston Villa | 5-0 | Birmingham City | (7-0) |
| Bradford City | 2-1 | Reading | aet (3-2) |
| Brentford | 4-3 | Blackburn Rovers | (5-6) |
| Chelsea | 2-2 | Scunthorpe United | (3-6) |
| Chester City | 0-4 | Nottingham Forest | (0-10) |
| Crystal Palace | 2-0 | Swindon Town | (4-1) |
| Leeds United | 3-1 | Peterborough United | (5-2) |
| Manchester United | 5-0 | Rotherham United | (6-0) |
| Newcastle United | 2-0 | Sheffield United | (2-3) |
| Plymouth Argyle | 3-6 | Manchester City | (3-7) |
| Scarborough | 3-1 | Portsmouth | (5-3) |
| Sheffield Wednesday | 3-1 | Blackpool | aet (3-3) |
| (Blackpool won on away goals) | |||
| Walsall | 1-3 | Liverpool | (1-4) |
| West Ham United | 2-1 | Sunderland | (5-1) |
| Wimbledon | 0-1 | Barnsley | (2-1) |
