The Riverhead Foundation for Marine Research and Preservation said the seal took a turn for the worse on Saturday and died on Monday.
The foundation had named him "Ozzy" and had been treating him with antibiotics.
The seal still had its umbilical cord attached when it was found on Feb. 12 at Montauk State Park.
The gray seal pup was about 3 feet long and 35 pounds. Adult males can weigh up to 800 pounds.