The 34-year-old's symptoms started with dry heaves immediately after he ate a Carolina reaper chilli during the contest in New York State.
He then developed intense neck and head pains along with "thunderclap" headaches which would last for several seconds at a time, according to the medical journal BMJ Case Reports.
The journal said the American had sought emergency care following the contest in 2016, but tests for several neurological conditions came back negative.
Doctors later diagnosed the man with a temporary brain condition called reversible cerebral vasoconstriction syndrome (RCVS), which is identified by the temporary narrowing of blood vessels to the brain.
The authors of the report said it was the first time the condition had been diagnosed after a patient had eaten a chilli.
RCVS usually occurs as a reaction to certain prescription medications or after taking illegal drugs, which brings on the the "thunderclap" headaches.
One of the authors of the article, Dr Kulothungan Gunasekaran of the Henry Ford Hospital in Detroit, said the diagnosis was "a big surprise to everyone".
The report, which warns of the dangers of eating extremely hot peppers, said the patient's symptoms eventually cleared up by themselves, with a CT scan taken five weeks after the incident showing his arteries had returned to normal size.
Dr Gunasekaran said: "We would recommend the general public be cautious when eating chilli peppers and to seek medical attention straight away if you develop symptoms like this."
Cayenne pepper has previously been linked to heart attacks, the study's authors said.
According to the Guinness World Records, the Carolina reaper has a sweet, fruity taste with a hint of cinnamon and chocolate - as well as being extremely hot.
The pepper - a cross between sweet Habanero and naga viper chillies - was named the hottest pepper on Earth last year.