Isaac, 25, underwent an MRI on Wednesday, when the injury was diagnosed. He will be sidelined after playing only 11 games this season. He missed two full years after suffering a torn ACL in the 2020 bubble.
"Our thoughts are with Jonathan, whose fortitude in dealing with adversity is unique," Magic president Jeff Weltman said in a statement. "Jonathan has worked extremely hard to return to the court this season and has demonstrated his impact on our team. We will be by his side as he focuses on the work ahead."
Isaac averaged 5 points, 4 rebounds and 1.2 steals per game in 11.3 minutes this season. He has played in 147 career games after the Magic chose him with the sixth overall pick in the 2017 NBA draft.