The experienced midfielder will return to his former club after an unsuccessful six-month spell at the Europa League holders, where he made just six appearances
The midfielder has signed a two-and-a-half year contract with the Istanbul giants, and will earn €1.2 million [£1m] for the remainder of this season, while receiving €2m [£1.7m] per annum after that.
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"I am extremely happy. I think all Fenerbahce fans will be be happy," the club's vice president Abdullah Kigili told their official website.
"When he was away, Fenerbahce missed him and he missed Fenerbahce. Emre will want to retire at Fenerbahce. We are pleased."
Emre joined Atletico from Fener at the start of this season, but failed to live up to expectations at the Vicente Calderon.
Therefore, the midfielder has now been allowed to return to his former club as he aims to relaunch his career after six disappointing months in La Liga.
The 32-year-old started his professional career with Galatasaray, and also represented Inter and Newcastle United before his first stint with Fener 2008.