The 34-year-old man had eaten one Carolina Reaper chilli in the contest in New York State.
The "crushingly painful" headaches came on in the next few days.
His experience has been published in the BMJ Case Reports as it is the first case to be associated with eating chilli peppers.
The doctor who reviewed his case has warned anyone eating hot chilli peppers to seek medical attention immediately if they experience sudden onset headaches.
"Thunderclap" headaches are caused by the sudden tightening of the vessels that supply blood to the brain, a condition known as reversible cerebral vasoconstriction syndrome (RCSV).
Immediately after eating at the contest, the man experienced dry heaves.
Severe neck pain developed over the next few days along with debilitating severe headaches, lasting just a few seconds at a time.
The pain was so bad he went to the emergency room and was tested for various neurological conditions, but the results were negative.
A CT scan showed that several arteries in his brain had constricted, leading doctors to diagnose him with RCVS.
BBC
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