The 25-year-old midfielder has penned a three-year deal that will keep him at the club until 30 June 2016.
"We wanted Johannes Flum because he's the sort of player that fits in perfectly with our philosophy and still has great potential to develop his game," said Eintracht sporting director Bruno Hübner.
The Black Forest native moved through the youth ranks at FC Rot-Weiß Weilheim, SV 08 Laufenburg and Freiburg, before joining regional outfit SC Pfullendorf in 2006.
Two years later, he was back at Freiburg, where he went on to score seven times in 91 league games after taking his top-flight bow in 2010. Flum also turned out 30 times in Bundesliga 2 and seven times in the DFB Cup, scoring once.