The 30-year-old, who was provisionally named in the Bosnia-Herzegovina squad for the 2014 FIFA World Cup last week, has been with the club since signing from Zagreb in 2009.
Mujdza has had an injury-marred 2013-14 campaign, making just seven Bundesliga appearances, but Freiburg have now confirmed the player will remain with the club for a sixth season.
Details of the deal remain under wraps, but Mujdza revealed his delight at having clarified his future.
"I feel totally comfortable in Freiburg and look forward to my sixth season at the sports club," he told the club's official website.
"I appreciate very much that the club has always supported me and I still have a lot to achieve with the club."
Mujdza has just one goal to his name from 90 league appearances for Freiburg.
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