The Turkish club have confirmed the deal on their website, with assistant coach Ismail Karat welcoming the 32-year-old back.
"Emre's quality is hard to find in a player," he said. "He is a player with great leadership quality, with self-confidence. Throughout his career he has gained experience which will be valuable to the team."
Emre has reportedly agreed a two-and-a-half year deal with Fener, for whom he played more than 100 games before joining Atletico last summer.
However, he failed to make much of an impact in Spain, making only a handful of appearances.