Police said the teen, Elijah Hinnant, and his friend were caught in a rip current while swimming Saturday.
Hinnant's friend, 16-year-old Tyreese Worsley, was rescued by a surfer and brought ashore.
He was taken to Carteret HealthCare before being airlifted to Vidant Medical Center in Greenville. Worsley is still listed in critical condition. He is a football player at Eastern Wayne High School.
The U.S. Coast Guard, along with Emerald Isle officials, searched for days trying to find the missing 17-year-old teen.
Police said that the teens were visiting Emerald Isle for the day, and that family members said neither were strong swimmers.
More: How to survive a rip current