18th April 1999
| Final | Wigan Athletic | 1-0 | Millwall |
23rd March 1999
| Northern Section Final 2nd Leg | Wrexham | 2-3 | Wigan Athletic |
16th March 1999
| Northern Section Final 1st Leg | Wigan Athletic | 2-0 | Wrexham |
| Southern Section Final 2nd Leg | Walsall | 1-1 | Millwall |
9th March 1999
| Southern Section Final 1st Leg | Millwall | 1-0 | Walsall |
8th March 1999
| Northern Section Semi-Final | 0-2 | Wigan Athletic |
23rd February 1999
| Northern Section Quarter-Final | 2-1 | FC Halifax Town |
16th February 1999
| Southern Section Semi-Final | Walsall | 1-1 | Cambridge United |
| Southern Section Semi-Final | Millwall | 1-0 |
| Northern Section Semi-Final | Lincoln City | 1-2 | Wrexham |
2nd February 1999
| Southern Section Quarter-Final | AFC Bournemouth | 1-1 | Millwall |
| Northern Section 2nd Round | 2-1 | Stoke City |
26th January 1999
| Northern Section Quarter-Final | Hartlepool United | 0-3 | Lincoln City |
| Northern Section Quarter-Final | Carlisle United | 0-3 | Wigan Athletic |
23rd January 1999
| Southern Section Quarter-Final | 0-1 |
19th January 1999
| Southern Section Quarter-Final | Cambridge United | 1-1 | Exeter City |
| Northern Section Quarter-Final | Wrexham | 3-2 | Chesterfield |
| Northern Section 2nd Round | Hartlepool United | 2-2 | Preston North End |
| Northern Section 2nd Round | Wigan Athletic | 3-0 |
| Northern Section 2nd Round | Scunthorpe United | 1-1 | Carlisle United |
| Southern Section Quarter-Final | Brentford | 0-0 | Walsall |
12th January 1999
| Northern Section 2nd Round | 0-2 | Chesterfield |
5th January 1999
| Northern Section 2nd Round | Hull City | 1-2 | Wrexham |
| Northern Section 2nd Round | Lincoln City | 1-0 | Mansfield Town |
| Southern Section 2nd Round | AFC Bournemouth | 5-1 | Peterborough United |
| Southern Section 2nd Round | Brighton & Hove Albion | 1-5 | Millwall |
| Southern Section 2nd Round | Cambridge United | 3-2 | Northampton Town |
| Southern Section 2nd Round | Exeter City | 3-1 |
| Southern Section 2nd Round | Luton Town | 0-3 | Walsall |
| Southern Section 2nd Round | Swansea City | 0-1 |
| Southern Section 2nd Round | 2-1 | Fulham |
| Southern Section 2nd Round | Wycombe Wanderers | 1-4 | Brentford |
| Northern Section 2nd Round | FC Halifax Town | 4-2 |
22nd December 1998
| Northern Section 1st Round | Notts. County | 0-1 | Hull City |
9th December 1998
| Southern Section 1st Round | Millwall | 2-0 | Cardiff City |
8th December 1998
| Southern Section 1st Round | Walsall | 2-2 | Bristol Rovers |
| Southern Section 1st Round | Swansea City | 4-1 | Barnet |
| Southern Section 1st Round | Shrewsbury Town | 0-1 | Wycombe Wanderers |
| Southern Section 1st Round | Peterborough United | 3-0 | Leyton Orient |
| Southern Section 1st Round | Brentford | 2-0 | Plymouth Argyle |
| Southern Section 1st Round | AFC Bournemouth | 2-0 | Reading |
| Northern Section 1st Round | Oldham Athletic | 0-1 |
| Northern Section 1st Round | Rotherham United | 0-3 | Wigan Athletic |
| Northern Section 1st Round | Manchester City | 1-2 | Mansfield Town |
| Northern Section 1st Round | Macclesfield Town | 0-1 | Wrexham |
| Northern Section 1st Round | 1-2 | Hartlepool United |
| Northern Section 1st Round | Burnley | 0-1 | Preston North End |
| Northern Section 1st Round | Blackpool | 0-2 | Stoke City |
5th December 1998
| Southern Section 1st Round | Colchester United | 1-5 |