(Associate Members) competition results from 1998/1999
A full listing of matches played in the competition throughout the season
| Southern Section Quarter-Final |
| Tuesday, 19th January 1999 |
| Brentford (LD3) | 0 | Walsall (LD2) | 0 | 2,048 |
| after extra time, 90 minutes 0-0, Walsall won 4-3 on penalties |
| Cambridge United (LD3) | 1 | Exeter City (LD3) | 1 | 2,758 |
| after extra time, 90 minutes 1-1, Cambridge United won 5-3 on penalties |
| Saturday, 23rd January 1999 |
| Torquay United (LD3) | 0 | Gillingham (LD2) | 1 | 3,121 |
| Tuesday, 2nd February 1999 |
| Bournemouth (LD2) | 1 | Millwall (LD2) | 1 | 5,339 |
| after extra time, 90 minutes 1-1, Millwall won 4-3 on penalties |
| Southern Section 2nd Round |
| Tuesday, 5th January 1999 |
| Bournemouth (LD2) | 5 | Peterborough United (LD3) | 1 | 3,398 |
| Brighton & Hove Albion (LD3) | 1 | Millwall (LD2) | 5 | 2,003 |
| Cambridge United (LD3) | 3 | Northampton Town (LD2) | 2 | 2,391 |
| Exeter City (LD3) | 3 | Southend United (LD3) | 1 | 1,143 |
| Luton Town (LD2) | 0 | Walsall (LD2) | 3 | 1,870 |
| Swansea City (LD3) | 0 | Gillingham (LD2) | 1 | 5,126 |
| Torquay United (LD3) | 2 | Fulham (LD2) | 1 | 2,596 |
| after extra time, 90 minutes 1-1, Torquay United won on golden goal rule |
| Wycombe Wanderers (LD2) | 1 | Brentford (LD3) | 4 | 2,010 |
| Northern Section 2nd Round |
| Tuesday, 5th January 1999 |
| Halifax Town (LD3) | 4 | York City (LD2) | 2 | 1,446 |
| Hull City (LD3) | 1 | Wrexham (LD2) | 2 | 2,331 |
| Lincoln City (LD2) | 1 | Mansfield Town (LD3) | 0 | 2,329 |
| Tuesday, 12th January 1999 |
| Darlington (LD3) | 0 | Chesterfield (LD2) | 2 | 1,391 |
| played at Chesterfield |
| Tuesday, 19th January 1999 |
| Hartlepool United (LD3) | 2 | Preston North End (LD2) | 2 | 1,205 |
| after extra time, 90 minutes 2-2, Hartlepool United won 4-3 on penalties |
| Scunthorpe United (LD3) | 1 | Carlisle United (LD3) | 1 | 1,507 |
| after extra time, 90 minutes 1-1, Carlisle United won 4-3 on penalties |
| Wigan Athletic (LD2) | 3 | Scarborough (LD3) | 0 | 1,693 |
| Tuesday, 2nd February 1999 |
| Rochdale (LD3) | 2 | Stoke City (LD2) | 1 | 7,361 |
| played at Stoke |
| Southern Section 1st Round |
| Saturday, 5th December 1998 |
| Colchester United (LD2) | 1 | Gillingham (LD2) | 5 | 1,742 |
| Tuesday, 8th December 1998 |
| Bournemouth (LD2) | 2 | Reading (LD2) | 0 | 2,666 |
| Brentford (LD3) | 2 | Plymouth Argyle (LD3) | 0 | 1,580 |
| Peterborough United (LD3) | 3 | Leyton Orient (LD3) | 0 | 1,801 |
| Shrewsbury Town (LD3) | 0 | Wycombe Wanderers (LD2) | 1 | 1,033 |
| after extra time, 90 minutes 0-0, Wycombe Wanderers won on golden goal rule |
| Swansea City (LD3) | 4 | Barnet (LD3) | 1 | 1,017 |
| Walsall (LD2) | 2 | Bristol Rovers (LD2) | 2 | 2,210 |
| after extra time, 90 minutes 2-2, Walsall won 5-4 on penalties |
| Wednesday, 9th December 1998 |
| Millwall (LD2) | 2 | Cardiff City (LD3) | 0 | 1,858 |
| Northern Section 1st Round |
| Tuesday, 8th December 1998 |
| Blackpool (LD2) | 0 | Stoke City (LD2) | 2 | 1,759 |
| Burnley (LD2) | 0 | Preston North End (LD2) | 1 | 3,366 |
| Chester City (LD3) | 1 | Hartlepool United (LD3) | 2 | 960 |
| after extra time, 90 minutes 1-1, Hartlepool United won on golden goal rule |
| Macclesfield Town (LD2) | 0 | Wrexham (LD2) | 1 | 804 |
| Manchester City (LD2) | 1 | Mansfield Town (LD3) | 2 | 3,007 |
| Oldham Athletic (LD2) | 0 | Darlington (LD3) | 1 | 2,133 |
| after extra time, 90 minutes 0-0, Darlington won on golden goal rule |
| Rotherham United (LD3) | 0 | Wigan Athletic (LD2) | 3 | 1,225 |
| Tuesday, 22nd December 1998 |
| Notts. County (LD2) | 0 | Hull City (LD3) | 1 | 1,109 |
