The 1999–2000 season was the 96th season in the history of FC Schalke 04 and the club's ninth consecutive season in the top flight of German football.

Schalke had a poor season, finishing in 13th place - only four points clear of relegation.

Squad at end of season ^[1]

Note: Flags indicate national team as defined under FIFA eligibility rules. Players may hold more than one non-FIFA nationality.

No. Pos. Nation Player 1 GK   GER Oliver Reck 2 DF   BEL Nico Van Kerckhoven 3 MF   CZE Radoslav Látal 4 DF   GER Yves Eigenrauch 5 MF   GER Sven Kmetsch 6 MF   GER Andreas Müller 8 MF   GER Thorsten Legat 9 FW   NED Youri Mulder 10 DF   GER Olaf Thon 11 FW   DEN Ebbe Sand 12 DF   NED Marco van Hoogdalem 13 GK   NOR Frode Grodås 14 MF   GHA Gerald Asamoah [notes 1] 15 DF   POL Tomasz Wałdoch

No. Pos. Nation Player 16 MF   GER Oliver Held 17 MF   GER Ünal Alpuğan 18 MF   NED Niels Oude Kamphuis 20 MF   CZE Jiří Němec 21 FW   BEL Émile Mpenza 22 GK   GER Mathias Schober 23 DF   GER Markus Happe 24 MF   BEL Marc Wilmots 25 DF   NED Johan de Kock 28 MF   GER Markus Kaya 29 GK   GER Toni Tapalović 30 MF   HUN Tamás Hajnal 31 MF   POR Sérgio Pinto 32 DF   HUN Krisztián Szollár

Note: Flags indicate national team as defined under FIFA eligibility rules. Players may hold more than one non-FIFA nationality.

No. Pos. Nation Player 7 FW   BEL Michaël Goossens ( Standard Liège) 8 MF   GER Ingo Anderbrügge (to Sportfreunde Siegen)

No. Pos. Nation Player 19 MF   GER Mike Büskens (to MSV Duisburg)