Jose Salvador Alvarenga, 37, was met by family members and officials after flying from the US.
The man was found washed up two weeks ago in the Marshall Islands. He says he left Mexico for a trip in a boat in December 2012 with a friend who died on board.
Jose Salvador Alvarenga apparently survived the 8,000 km (5,000-mile) ordeal by catching fish, birds and turtles with his bare hands.
For fluids, he claimed to have drunk urine, rainwater and the blood of birds.
Jose Salvador Alvarenga was rescued on January 30 by people living on the island of Ebon Atoll.
He was found dehydrated and suffering from back pain and swollen joints.
Jose Salvador Alvarenga landed at El Salvador’s international airport, near the capital San Salvador, at about 20:00 local time on Tuesday after flying from Los Angeles.
At the airport’s VIP lounge, Jose Salvador Alvarenga was met by El Salvador’s foreign minister and other government officials.
Dozens of journalists also gathered at the airport.
On his way from the Marshall Islands Jose Salvador Alvarenga had long stopovers in Hawaii and Los Angeles, where doctors had checked his health and ability to continue the trip.
Jose Salvador Alvarenga will now undergo further checks before a decision is taken whether he should stay overnight in a local hospital or can return to his coast fishing village of Garita Palmera.
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