The legendary two-time Champions League winner used to suffer from third season syndrome, but it appears he's hit the blocks after just six months in Turkey.
Arriving to much fanfare in June, the Portuguese was backed heavily in the transfer window with a Turkish Super Lig-leading £25million net spend, and hopes were high for a title win after missing out to Istanbul rivals Galatasaray last season.
However, back-to-back losses have left him in a precarious position, with AS in Spain claiming pre-match that another defeat to Athletic Bilbao would 'put his future in doubt'.
That result came to fruition, with Fenerbahce downed 2-0 by the Spanish Copa del Rey champions as an in-form Inaki Williams scored both goals.
The result leaves the Istanbul giants on just eight points after six games in the Europa League this season, with the cut off for qualification for the next round currently five points with 34 teams to play on Thursday.
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Fenerbahce began the season in Champions League qualifying, but a win over Swiss side Lugano was followed by defeat to Lille, delivering Mourinho an early blow.
Things have been inconsistent ever since, and some often unpleasant comments in the media have strained things even further.
That ill-discipline has extended to the pitch too, where there were again many moments of petulance.
Against Athletic, Mert Muldur was sent off for a second yellow card in the home match in the 69th minute, and former Manchester United loanee Sofyan Amrabat was fortunate not to join him in receiving his marching orders.
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The Morocco midfielder, who spent last season on an uneventful loan at Old Trafford, made a late challenge on Oihan Sancet in stoppage time.
When Sancet turned to ask for an explanation, he was grabbed by the neck by Amrabat in aggressive scenes.
However, the referee instead opted to give both players a yellow card, saving Fenerbahce's blushes ahead of their final two league phase matches against Lyon and Danish club Midtjylland.
The defeat follows a painful 1-0 defeat to Istanbul rivals Besiktas last time out in the league.
Mourinho's side had just built up a head of steam to record seven wins in eight games and catch up with leaders Galatasaray, but that gap has now extended to three points.
Mourinho also created headlines pre-match when he was asked to clarify comments directed at Manchester City's Pep Guardiola when he said his Premier League title wins were 'clean'.
"It's not true that I want Man City to be relegated," Mourinho said. "It's true that I like justice, and many times small clubs are punished by going €5, €10 over budget and the rules for Financial Fair Play.
"For example, I suffered in Roma three years with great limitations about it. I don't think it's fair that the big sharks - when I say sharks, I say financial sharks -- they always find a way to escape the rules.
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"I'm just a football man, a man that loves football, more than being a professional football man I am very passionate, I just like justice in football. But apart from that, no bad feelings."