In the following two seasons, Tilson took Southend to two consecutive promotions from League Two to the Championship. Southend also reached another Football League Trophy Final in 2005, but lost to Wrexham. Tilson's success saw him linked with jobs at West Bromwich Albion and Norwich City, but he remained with Southend. In November 2006, Southend achieved a notable victory over eventual Premier League champions Manchester United in the League Cup, but were relegated from the Championship at the end of the 2006–07 season.