Schneider joined VfB Stuttgart as a 10-year-old, and progressed through the youth teams, making his breakthrough in the 1991–92 season. He made two appearances that year, deputising for Uwe Schneider (no relation) as the club won the Bundesliga title. He spent the next couple of years back in Stuttgart's reserve team, and it wasn't until August 1994 that he made his third Bundesliga appearance, when he replaced Marc Kienle in a 2–2 draw with 1. FC Köln at the Gottlieb-Daimler-Stadion. Over the next seven years he established himself as a regular member of Stuttgart's first-team, playing alongside experienced defenders such as Thomas Berthold, Zvonimir Soldo and Frank Verlaat, and such were his performances that he was almost called up to the German national team by then coach Berti Vogts. In 1997 Stuttgart won the DFB-Pokal, and Schneider played in the final, replacing Matthias Hagner for the last 20 minutes of the victory over FC Energie Cottbus. The following year he was in the starting line-up for the UEFA Cup Winners' Cup Final, but Stuttgart lost 1–0 to Chelsea.