The former Arminia Bielefeld boss replaces Jörg Böhme, after putting pen to paper on a deal that will keep him at the club until 2016.
'Keen and ambitious'
"He's just the type of coach we were looking for," said sporting director Roland Benschneider. "Stefan Krämer is keen and ambitious, and he’s helped Bielefeld win promotion to Bundesliga 2."
Assistant coach Rene Rydlewicz will take charge of Cottbus' final game of the 2013/14 campaign away at FC Ingolstadt 04 on Sunday afternoon.