In January, Mustafi joined Schalke but was unable to help them escape the drop as they finished with just 16 points from 34 games.
Kicker holds annual awards at the end of the season, where professionals anonymously vote on various things.
Robert Lewandowski was named as player of the year with 74 per cent of the votes and best newcomer went to his Bayern team-mate, 18-year-old Jamal Musiala.
Kicker also pays attention to the bottom end of the scale however.
Mustafi only joined the club in February after his Arsenal contract was terminated but still claimed his award for "relegated player of the season" with 13.3% of the overall vote.