Keith Stevens and Alan McLeary guided Millwall to their first ever official Wembley appearance. The opponents were Wigan Athletic in the Auto Windscreens Final. However, Millwall, who were watched in front of 49,000 of their own fans, missed numerous opportunities to win the match, and lost by a single injury time goal. Millwall also lost on aggregate to Wigan in the 2nd Division play-off semi finals in 1999.

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Mark McGhee was appointed as Millwall's new manager in September 2000, and eight months later the club gained promotion as Division Two champions after 5 years in the lower tier of the league. Winning the opening match of the season 4-0 at home to Norwich City set the team up well for a great season in which Millwall qualified for the Division One playoffs, but suffered defeat to eventual winners Birmingham City 0 - 1 in the semi finals. This resulted in missing out on a second successive promotion, which would have given them a birth in the Premiership. Millwall missed out on a playoff position in 2002-03 and McGhee was sacked soon after the beginning of the 2003-04 season.