After ruling out various neurological conditions, a CT scan showed that several arteries in the patient's brain had constricted.
The doctor who reviewed his case has warned anyone eating hot chilli peppers to seek medical attention immediately if they experience sudden onset headaches.
The unnamed man began dry heaving as soon as he swallowed the Carolina Reaper pepper.
The man then developed intense neck and head pain, and for several days experienced brief but intense "thunderclap" headaches.
The condition - a temporary artery narrowing often accompanied by "thunderclap" headaches - can be caused by certain prescription medications or illegal drugs.
The Carolina Reaper, a hybrid of the ghost pepper and the red habanero, is estimated to be about 300 times as hot as the spiciest jalapeno and holds the record as the hottest pepper in the world.
The doctors treating the man said: "Given the development of symptoms immediately after exposure to a known vasoactive substance, it is plausible that our patient had RCVS secondary to the Carolina Reaper".
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"Thunderclap" headaches are medical emergencies, because they can signal bleeding in the brain. A bird's eye chilli - small and hot enough for most spice-lovers - contains up to 225,000.
But in this instance, the pepper's spiciness caused the blood vessels supplying his brain to temporarily thin, producing the same painful outcome. This is the first reported case of this sort of reaction to eating a hot pepper.
The result of a sudden constriction of the coronary artery is a heart attack, the doctors said.
Some people like to do this sort of thing in private - testing their powers of endurance for reasons only they know - while for others competing against fellow hot-pepper fanatics is the name of the game.
Although a situation like this is rare and possibly the first to be documented, it is important to note that it is possible, said Gunasekaran, who co-authored a description of the man's symptoms, diagnosis, treatment and followup that was published Monday in BMJ Case Reports.
"Our patient's symptoms improved with supportive care, he had no further thunderclap headaches", the report said.