The Croat was a set and a break down to Roger Federer when he appeared to be crying at the change of ends at 3-0 down.
Cilic put a towel over his head and stared towards the ground as he bid to regather himself.
Fans rushed to Twitter to give their verdict on the incident.
One wrote: "That was tough watching Cilic crying 🙁 #Wimbledon."
Another said: " You've got this! Don't worry about getting upset just I hope you take all the time you need. I hope you are okay don't let it get to you."
Marin Cilic broke down in tears during the Wimbledon final against Roger Federer
Marin Cilic put a towel over his head as he tried to compose himself
A fellow fan added: "Sending love and strength to Marin Cilic. Things are not looking too good for him right now.
While another tweeted: "Aww, really feel for @cilic_marin something clearly wrong with him on court #Wimbledon2017 #WimbledonFinals #keepgoing #YouCanDoIt."
A fellow fan reasoned: "Perhaps some sensitivity until we know what happened with @cilic_marin #WimbledonFinal."
Federer romped the set to take a 6-4 6-1 lead as he cloed in on his eighth Wimbledon title.
The doctor and physio returned at the end of the set and spoke to Cilic for a prolonged period of time.
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Marin Cilic breaks down in TEARS during Wimbledon 2017 final Sun, July 16, 2017
Marin Cilic broke down in tears during the Wimbledon final against Roger Federer.
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Commentator Andrew Castle said: "Whether we need the doctor, supervisor and medical attention, we cant tell.
"He started crying a few minutes ago. It was a horrible situation.
"You want the ground to open up and swallow you up in situations like this.
"He's geting hammered."
Cilic then had his left foot taped up before the start of the third set with his exact problem a mystery.
Marin Cilic was a set and a break down to Roger Federer when he began to well up
Former British tennis star Tim Henman added: "Cilic is walking around in front of our commentary box, and one thing he normally does well is how he's dealt with the nerves.
"He's looking completely lost out there
"His opponent is not helping things."
A medical timeout was called shortly after the end of the second set as Cilic got prolonged treatment.