The 62-year-old's departure comes two days after the Turkish club failed to qualify for the Champions League league phase following defeat to Benfica in the play-off round.
Mourinho was appointed to the role ahead of the 2024-25 season and Fenerbahce finished second in the Super Lig last term, 11 points adrift of rivals Galatasaray.
"We have parted ways with Jose Mourinho," read a club statement.
"We thank him for his efforts for our team and wish him success in his future career."
Mourinho's spell in Turkey has been turbulent, including an incident in April when he grabbed the nose of Galatasaray coach Okan Buruk in the Istanbul derby — earning a three-match ban and a fine.
He was also handed a four-match ban in February after making an incendiary comment after a league match against Galatasaray.
Mourinho was once one of the most sought-after coaches in world soccer, after trophy-winning spells at Porto, Chelsea, Inter Milan, Real Madrid and Manchester United, but his status is on the wane.
The two-time Champions League winner has not coached in the main stage of the marquee competition for six seasons.
Meanwhile, Fenerbahce's absence from the Champions League now stretches to 17 seasons.
The news comes a day after Ole Gunnar Solskjaer, who replaced Mourinho as United manager in 2018, was sacked by Fener's Super Lig rivals Besiktas.
- with The AP
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