Mourinho has been axed by Fener after they lost their Champions League playoff with Benfica.
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The former Chelsea, Real Madrid and Inter Milan coach moved to Istanbul in 2024 following two years with Serie A club Roma.
The Portuguese managed the Turkish club in 62 games, winning 37 times - a win percentage of 59.68%.
However, after finishing runners-up to rivals Galatasaray last season and failing in this week's playoff, Fener's board chose to part ways today.
"We thank him for his efforts for our team until today and wish him success in his future career," the club said in a statement.