Cilic's eyes welled up and he started crying at 6-4 3-0 down and was spoken to on court by a doctor.
It was unclear what exactly had gone wrong with the doctor returning again at the end of the set, which he lost 6-1.
A medical timeout was called at the end of the set, during which Cilic had strapping removed and reapplied on his foot.
Boris Becker, working for the BBC, believes a blister was the cause of his tears and said "We've got an explanation of what went wrong.
Marin Cilic teared up during the Wimbledon final
Marin Cilic put a towel over his head to try and compose himself
"He had a huge blister on his foot and couldn't walk anymore.
"I hope they've fixed it.
"I just hope for the sake of the spectators the final will be more of a match now."
Appearing alongside Becker in the commentary box, Andrew Castle said: "There's a certain amount of turmoil in his head now.
"He's a little embarrassed. It's only been going on an hour and 18 minutes.
Marin Cilic breaks down in TEARS during Wimbledon 2017 final Sun, July 16, 2017
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Marin Cilic broke down in tears during the Wimbledon final against Roger Federer.
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"He's a little disappointed with how hes playing so far."
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."
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