28th May 1989
| Final | Bolton Wanderers | 1-4 |
18th April 1989
| Northern Section Final 2nd Leg | Blackpool | 1-1 | Bolton Wanderers |
| Southern Section Final 2nd Leg | Wolverhampton Wanderers | 0-2 |
12th April 1989
| Southern Section Final 1st Leg | 1-2 | Wolverhampton Wanderers |
11th April 1989
| Northern Section Final 1st Leg | Bolton Wanderers | 1-0 | Blackpool |
22nd March 1989
| Southern Section Semi-Final | 0-2 | Wolverhampton Wanderers |
21st March 1989
| Northern Section Semi-Final | Blackpool | 1-0 |
| Southern Section Semi-Final | Brentford | 0-1 |
| Northern Section Semi-Final | Crewe Alexandra | 1-2 | Bolton Wanderers |
22nd February 1989
| Southern Section Quarter-Final | Bristol Rovers | 0-1 |
21st February 1989
| Northern Section Quarter-Final | Bolton Wanderers | 3-1 | Wrexham |
| Northern Section Quarter-Final | FC Halifax Town | 0-2 | Blackpool |
| Northern Section Quarter-Final | Huddersfield Town | 1-2 |
| Southern Section Quarter-Final | Wolverhampton Wanderers | 3-1 | Northampton Town |
| Southern Section Quarter-Final | Chesterfield | 0-1 | Brentford |
| Northern Section Quarter-Final | Wigan Athletic | 0-1 | Crewe Alexandra |
14th February 1989
| Southern Section Quarter-Final | Colchester United | 0-1 |
24th January 1989
| Southern Section 1st Round | Bristol Rovers | 2-1 | Cardiff City |
| Southern Section 1st Round | Wolverhampton Wanderers | 3-0 | Bristol City |
18th January 1989
| Southern Section 1st Round | Reading | 2-3 |
17th January 1989
| Southern Section 1st Round | Brentford | 2-0 | Notts. County |
| Southern Section 1st Round | 3-0 |
| Northern Section 1st Round | Blackpool | 4-3 | Rotherham United |
| Northern Section 1st Round | Preston North End | 0-1 | Bolton Wanderers |
| Southern Section 1st Round | Northampton Town | 2-1 |
| Northern Section 1st Round | Grimsby Town | 1-3 | Huddersfield Town |
| Northern Section 1st Round | Burnley | 1-1 | Crewe Alexandra |
| Northern Section 1st Round | FC Halifax Town | 3-0 |
| Northern Section 1st Round | Wrexham | 2-1 | Sheffield United |
| Southern Section 1st Round | Chesterfield | 4-2 | Cambridge United |
| Southern Section 1st Round | Colchester United | 3-1 | Leyton Orient |
| Northern Section 1st Round | 0-1 | Wigan Athletic |
10th January 1989
| Southern Section Preliminary Round Group One | Aldershot Town | 1-3 | Leyton Orient |
7th January 1989
| Northern Section 1st Round | 3-1 |
21st December 1988
| Southern Section Preliminary Round Group Seven | Peterborough United | 0-2 | Northampton Town |
| Northern Section Preliminary Round Group Eight | 1-2 | Wrexham |
20th December 1988
| Northern Section Preliminary Round Group One | 1-0 | Bolton Wanderers |
| Southern Section Preliminary Round Group Four | Colchester United | 2-1 |
| Northern Section Preliminary Round Group Six | FC Halifax Town | 1-0 | Huddersfield Town |
| Southern Section Preliminary Round Group Two | 3-1 | Cardiff City |
14th December 1988
| Northern Section Preliminary Round Group Five | 4-0 |
| Southern Section Preliminary Round Group Eight | Exeter City | 1-1 | Bristol Rovers |
13th December 1988
| Northern Section Preliminary Round Group One | Preston North End | 4-0 |
| Northern Section Preliminary Round Group Two | Rotherham United | 2-1 |
| Northern Section Preliminary Round Group Eight | Sheffield United | 2-2 |
| Northern Section Preliminary Round Group Four | Hartlepool United | 0-2 |
| Northern Section Preliminary Round Group Six | Huddersfield Town | 1-0 | Scunthorpe United |
| Northern Section Preliminary Round Group Three | Crewe Alexandra | 1-1 |
| Northern Section Preliminary Round Group Seven | 0-2 | Wigan Athletic |
| Southern Section Preliminary Round Group Six | Wolverhampton Wanderers | 5-1 | Port Vale |
10th December 1988
| Southern Section Preliminary Round Group Five | Chesterfield | 2-1 | Mansfield Town |
| Southern Section Preliminary Round Group Three | 2-1 | Fulham |
6th December 1988
| Northern Section Preliminary Round Group One | Bolton Wanderers | 1-0 | Preston North End |
| Northern Section Preliminary Round Group Two | 1-1 | Grimsby Town |
| Southern Section Preliminary Round Group Eight | Bristol City | 2-0 | Exeter City |
| Southern Section Preliminary Round Group Two | Cardiff City | 2-0 | Swansea City |
| Southern Section Preliminary Round Group One | Leyton Orient | 1-1 | Reading |
| Northern Section Preliminary Round Group Seven | Blackpool | 2-0 |
| Northern Section Preliminary Round Group Six | Scunthorpe United | 1-2 | FC Halifax Town |
| Southern Section Preliminary Round Group Five | Notts. County | 1-1 | Chesterfield |
| Northern Section Preliminary Round Group Five | 3-2 | Carlisle United |
5th December 1988
| Northern Section Preliminary Round Group Three | 2-1 |
| Northern Section Preliminary Round Group Eight | Wrexham | 1-1 | Sheffield United |
30th November 1988
| Southern Section Preliminary Round Group Four | Lincoln City | 1-2 | Colchester United |
| Southern Section Preliminary Round Group Six | 2-2 | Wolverhampton Wanderers |
| Southern Section Preliminary Round Group One | Reading | 5-2 | Aldershot Town |
29th November 1988
| Southern Section Preliminary Round Group Three | Brentford | 2-0 |
| Southern Section Preliminary Round Group Two | Swansea City | 1-0 |
| Southern Section Preliminary Round Group Five | Mansfield Town | 1-1 | Notts. County |
| Northern Section Preliminary Round Group Two | Grimsby Town | 1-0 | Rotherham United |
| Southern Section Preliminary Round Group Seven | Cambridge United | 2-2 | Peterborough United |
| Northern Section Preliminary Round Group Four | Burnley | 3-0 | Hartlepool United |
| Northern Section Preliminary Round Group Five | Carlisle United | 1-1 |
28th November 1988
| Northern Section Preliminary Round Group Three | 1-1 | Crewe Alexandra |
23rd November 1988
| Southern Section Preliminary Round Group Eight | Bristol Rovers | 1-0 | Bristol City |
22nd November 1988
| Southern Section Preliminary Round Group Three | Fulham | 0-2 | Brentford |
| Southern Section Preliminary Round Group Four | 2-1 | Lincoln City |
| Northern Section Preliminary Round Group Seven | Wigan Athletic | 1-2 | Blackpool |
| Southern Section Preliminary Round Group Seven | Northampton Town | 1-1 | Cambridge United |
| Northern Section Preliminary Round Group Four | 0-2 | Burnley |
21st November 1988
| Southern Section Preliminary Round Group Six | Port Vale | 1-1 |