Joining Hagel on the trip from Washington were Army Secretary John McHugh and Army Chief of Staff Gen. Ray Odierno.
The remains of every U.S. military member killed overseas are flown to Dover for processing. Family members often attend the arrivals, but high-ranking Pentagon officials usually do not.
Hagel's trip to Delaware came amid congressional criticism over the suspension of $100,000 death benefit payments to families of fallen soldiers, which the Pentagon blames on the government shutdown.
The family of 24-year-old Pfc. Cody Patterson of Oregon allowed members of the media to witness the return of his remains Wednesday.
Burns reported from Washington.