Phoenix Thoroughbreds ownership group announced that the England-based colt developed a fever over the weekend and will not make the journey to Churchill Downs.
The tight end, who is part-owner of the 3-year-old horse, tweeted about situation.
"It's unfortunate Gronkowski the horse will not be able to race in the upcoming Kentucky Derby due to an illness," he wrote. "I fully support what is best for the horse. I know he will come back strong and healthy and I am excited to see him race again very soon."
The ownership group tweeted that the horse was treated with antibiotics and "is doing well."
"We very much regret that #Gronkowski will miss the @KentuckyDerby after spiking a fever over the weekend and being treated with antibiotics," the global horse racing investment fund wrote. "He can't make the long journey to Louisville but is doing well."
Trainer Jeremy Noseda's family are Patriots fans, so they named the horse after Gronkowski.
The equine was undefeated in three races this year.
The Kentucky Derby will be run at Churchill Downs on May 5.