The NTSB investigation took four years and was the only instance when a crashed plane had been fully rebuilt, but the investigation could only come to a general conclusion that the explosion began in the center fuel tank and the source of ignition could not be determined. The results of the investigation eventually led to a new safety requirement for a device that removes oxygen from an empty fuel tank, which was thought to have accumulated and ignited in Flight 800's center tank, which would have been mostly empty and only used for long flights. When the new rule was fully enacted in 2008, the National Air Traffic Controllers Association questioned why the oxygen removal process only applied to center fuel tanks like Flight 800's and not wing-mounted fuel tanks, a change which had also been recommended by the NTSB.

A memorial to those lost was built near the crash site at Smith Point County Park that includes the flags of the 13 home countries of those killed in the crash, and the rebuilt Boeing 747 plane is now located in Virginia and used to train investigators.