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 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.
Carlisle United, Chesterfield, Halifax Town, Lincoln City, Rochdale, Scarborough, Scunthorpe United and York City from the North section all received byes.