He arrived in New York on a flight from Ciudad Juarez.
Mr Guzman, who could face life in a US prison, is wanted on charges of drug trafficking and smuggling vast amounts of drugs into the country.
The leader of the Sinaloa cartel was facing two extradition requests - one from California and another from Texas.
Last year he was moved to a prison in Ciudad Juarez, which lies just across the border from El Paso in Texas, but authorities at the time denied the transfer was a precursor to extradition.
Mr Guzman has been fighting to stay in Mexico but his appeals were rejected.
He was under close watch, having previously broken out of two Mexican high-security jails.
He is now expected to appear in a US federal court in Brooklyn on Friday
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