Dortmund's form improved during the 1998–99 season and they climbed to 4th, qualifying again for the Champions League.

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 Jens Lehmann 3 DF  GER René Schneider 4 MF  YUG Miroslav Stević 5 DF  GER Jürgen Kohler 7 DF  GER Stefan Reuter 8 MF  GER Christian Nerlinger 9 FW  SUI Stéphane Chapuisat 10 MF  GER Andreas Möller 11 FW  GER Heiko Herrlich 12 GK  GER Wolfgang de Beer 13 FW  GHA Bashiru Gambo 14 FW  BIH Sergej Barbarez 15 DF  NED Alfred Nijhuis 16 DF  GER Martin Kree

No. Pos. Nation Player 17 DF  BRA Dedé 18 MF  GER Lars Ricken 19 DF  GER Thomas Hengen 20 MF  GER Thomas Häßler 21 FW  GER Christian Timm 22 FW  GHA Ibrahim Tanko 24 FW  NED Harry Decheiver 26 MF  GER Frank Riethmann 27 DF  AUT Wolfgang Feiersinger 29 MF  RUS Vladimir But 30 FW  TOG Bachirou Salou 32 DF  GER Manfred Binz 33 DF  GER Karsten Baumann

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 Stefan Klos (to Rangers) 2 MF  GER Knut Reinhardt (to 1. FC Nürnberg) 4 MF  GER Steffen Freund (to Tottenham Hotspur)

No. Pos. Nation Player 6 MF  GER Matthias Sammer (retired) 31 DF  NOR Steinar Pedersen (to Lillestrøm)