The 34-year-old American patient required emergency treatment for excruciating headaches and neck pain after eating the “Carolina Reaper”, which is as strong as military-grade pepper spray.
A scan showed several arteries in his brain had temporarily narrowed, causing severe episodic "thunderclap" headaches.
Doctors warned that taking part in hot chilli contests could have unexpected consequences, as they published details of the incident in journal BMJ Case Reports.
Produced by The PuckerButt Pepper Company, the Carolina Reaper is the current Guinness World Record holder for the hottest chilli and has been known to reach 2.2 million on the Scoville Scale.
That means one drop of its oil would be detectable in 2.2 million drops of water.
A Jalapeno pepper typically rates between 2,500 to 5,000 units on the scale.
The patient, who has not been identified, immediately began dry heaving after sampling the chilli, the US authors said in the paper.
Over the following days, he developed "intense" neck pain and headaches, each of which lasted just a few seconds.
The pain was so severe that he sought emergency treatment and he was tested for multiple neurological conditions, the results of which all came back negative.
But a CT scan showed several arteries in the man's brain had constricted and he was diagnosed with reversible cerebral vasoconstriction syndrome (RCVS).
The condition - a temporary artery narrowing often accompanied by "thunderclap" headaches - can be caused by certain prescription medications or illegal drugs.
However, the authors said this is the first time it has been linked with eating chilli peppers.
The man's symptoms cleared up on their own and a CT scan five weeks later showed his arteries had returned to their normal width, the authors said.
Dr Kilothungan Gunasekaran, who treated the patient at the Department of Internal Medicine, Bassett Medical Center, New York, said: “"The pain was excruciating.”
“No cases of RCVS secondary to peppers or cayenne have been previously reported, but ingestion of cayenne pepper has been associated with coronary vasospasm and acute myocardial infarction.”
Last year the Carolina Reaper was overtaken as the hottest chilli ever recorded after a Welsh fruit farmer, Mike Smith, “accidentally” created the Dragon’s Breath, which registered 2.48 million on the Scoville heat scale.
The chilli tree was grown as an entry for the Chelsea Flower Show.