In January 2003, he moved to FC St. Pauli and was their first-choice keeper until the end of the 2002–03 season, appearing in sixteen 2. Bundesliga games. The club was relegated to the Regionalliga at the end of the season, and Müller moved on to then newly promoted 2. Bundesliga side SSV Jahn Regensburg for the 2003–04 season, and made four 2. Bundesliga appearances for the club at the beginning of the season.
