The infamous cartel boss, whose real name in Joaquin Guzman, was seen being led into an aircraft hangar in Ronkonkoma, Long Island, on Thursday night.
The 59-year-old appeared clean shaven in a beige jacket as he was flanked by guards.
The Mexican drug baron faced two extradition bids, one in California for drug distribution and another in Texas on charges that include murder and money laundering.
Approving the extradition in May, Mexico’s foreign ministry said in a statement that the US government had given ‘enough guarantees that the death penalty will not be applied’.
But his legal team had hoped to stop his extradition, with his attorney Andres Granados filing papers to the courts in Mexico City.
It had been believed it could take six months to issue its ruling, before a likely appeal to the Supreme Court.
The S The fugitive was caught after a fierce gun battle in Los Mochis, a city in northern Sinaloa, during which five of his men were killed.
He was one of six people arrested after a four-hour operation.
Mexican marines who led the mission came under heavy gunfire after cornering the gang in a house in the city.
Six months earlier he disappeared through a 2ft wide hole in descending some 32 feet down a ladder from the Altiplano prison - 55 miles west of Mexico City .
The tunnel, which took a year to dig and was estimated to have cost £4million, was found equipped with ventilation ducts, running electricity to power strip lighting and stairs.