The thoroughbred - christened Usain Colt - has already lived up to its star name, winning at Newbury racecourse last year in only its second race.
When the royal met the sprinter during a training session in Kingston, Jamaica, he asked the athlete to pose for a picture with the horse and sign it.
Bolt joked afterwards: "For me it's interesting, but to have a racehorse named after you by someone who owns it like Prince Harry for me is an honour.
"He's going to do great, takes time, work his way up."
It appears Harry has picked up his love of horses from the Queen, who is a passionate horseowner and breeder whose thoroughbreds have won a string of classic races over the years.
The animal is owned by Ascot Racecourse and it is thought Harry has joined the Birdcage Racing Club run by Ascot, whose 100 members pay an annual membership fee to share the prize money earned by Usain Colt.
Some of the prince's friends, and Marcus Mumford from the group Mumford & Sons, are also members and have the same stake.
The prince's bay colt was sired by the aptly named Royal Applause and is put through its paces by Richard Hanson, who trains the Queen's horses.