Family members say 17-year-old Haris Suleman was piloting the single-engine Hawker Beechcraft airplane, with his father, Barber Suleman, along for the ride.
Their aircraft had just taken off from Pago Pago in American Samoa Tuesday night when it crashed.
The Sulemans were on their way back to Indiana where they departed on June 19. They had made stops across Europe, Africa, Asia and the South Pacific.
The U.S. Coast Guard says it recovered the remains of the younger Suleman. Authorities continue to search for his father.
The father and son were using the trip to raise money for the Citizens Foundation. The nonprofit builds schools in Pakistan.