The New York State Health Commissioner confirmed it happened about 25 minutes after the individual was vaccinated and following the required 15-minute observation period.
Dr. Howard Zucker said initial indications are the man, who was in his 70s, did not have an allergic reaction to the vaccine.
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On-site security and first responders got to the man in seconds, but he passed away a short time later at a hospital.
Health officials say it is important to note that just because someone died, it does not mean it is related to the vaccine.
"Public health experts agree, the vaccine is safe, and together with continued vigilance including wearing a mask and social distancing, it will bring an end to this pandemic," Zucker said. "I encourage all eligible New Yorkers to get vaccinated."
The Javits Center opened as a vaccine mega-site in early January.
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