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.