In 2003 Dennis Wise, ex-Chelsea and England player, became caretaker, and went on to perform heroics as player-manager, of the club. In his debut season in charge Wise guided the club to the first FA Cup final in their history. Millwall took to the field at the Millennium Stadium they were only the second club from outside the top flight to star in the final since 1982, and were the first team from outside the Premiership to reach the final since its foundation in 1992. They were also missing no fewer than 16 players from their squad due to suspension or injury. They played the Cup final on May 22, 2004, suffering defeat 3-0 to Manchester United. As Manchester United had already qualified for the Champions League, Millwall were guaranteed playing in the 2004/05 UEFA Cup. Millwall midfielder Curtis Weston, substituted for Wise with two minutes to play, became the youngest Cup Final player in history at 17 years 119 days, beating the 125 year old record of James F. M. Prinsep. Dennis Wise also insisted that the injured Tony Warner and Kevin Muscat be presented with medals.In the 2004/05 UEFA Cup, Millwall suffered a 4-2 on aggregate in the first round proper, to Hungarian Champions Ferencváros, with Wise scoring both Millwall goals. Millwall put up a great fight in both games, but the Hungarian title winners were too strong. Surprisingly, whilst Millwall were seeded, Ferencvaros were not. Millwall may have had an easier draw, against Chechnyan minnows Terek Grozny. If Millwall had beaten them, then they would have made it into the group phase of the competition, where they would have met some of Europe's elite, including teams such as Lazio and Schalke. This would have been a great chance for Millwall on and off the playing field. In 2005 Theo Paphitis announced that he was stepping down as chairman of the club with Jeff Burnige to replace him from May 2005. At the end of the 2004-05 season, manager Dennis Wise announced that he was departing as he was not able to form a working relationship with the new chairman.

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On the 21st June 2005, footballing legend, Steve Claridge was announced as the new player/manager of Millwall FC. However, when Burnige then left just 2 months after taking up the post, it was announced on 27 July that Claridge had been dismissed after 36 days, without ever taking charge of the club in a competitive tie.