| Auto Windscreens Shields | |
|---|---|
| Tournament details | |
| Country |  England  Wales | 
| Teams | 48 | 
| Final positions | |
| Champions | Wigan Athletic | 
| Runner-up | Millwall | 
| Tournament statistics | |
| Matches played | 49 | 
The Football League Trophy 1998–99, known as the Auto Windscreens Shield 1998–99 for sponsorship reasons, was the 16th staging of the Football League Trophy, a knock-out competition for English football clubs in Second and Third Division. The winners were Wigan Athletic who beat Millwall 1–0 in the final.
The competition began on 5 December 1998 and ended with the final on 18 April 1999 at the Wembley Stadium.
In the first round, there were two sections: North and South. In the following rounds each section gradually eliminates teams in knock-out fashion until each has a winning finalist. At this point, the two winning finalists face each other in the combined final to determine the winners of the Football League Trophy.
First round
Carlisle United, Chesterfield, Halifax Town, Lincoln City, Rochdale, Scarborough, Scunthorpe United and York City from the North section all received byes.
Brighton & Hove Albion, Cambridge United, Exeter City, Fulham, Luton Town, Northampton Town, Southend United and Torquay United from the South section all received byes.
| Northern Section
 | Southern Section
 
 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Second round
| Northern Section
 | Southern Section
 
 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Quarter-finals
| Northern Section
 | Southern Section
 
 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Area semi-finals
| Northern Section
 | Southern Section
 
 | |||||||||||||||||||||||||||||
Area finals
Northern Area final
| Wigan Athletic | 2–0 | Wrexham | 
|---|---|---|
| Sharp  59' Barlow  71' | 
| Wrexham | 2–3 | Wigan Athletic | 
|---|---|---|
| Brammer  37' Edwards  59' Ridler  | Haworth  2'  52' O'Neill  88' | 
Wigan Athletic beat Wrexham 5–2 on aggregate.
Southern Area final
| Walsall | 1–1 | Millwall | 
|---|---|---|
| Eyjólfsson  88' | Sadlier  37' | 
Millwall beat Walsall 2–1 on aggregate.
Final
| Millwall | 0–1 | Wigan Athletic | 
|---|---|---|
| Report | Rogers  90+3' | 
|      Millwall |      Wigan Athletic | 
| 
 | 
 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| MATCH RULES 
 | 


