Mexico's Foreign Relations Department announced Guzman was handed over to U.S. authorities for transportation to the U.S. on Thursday, the last day of President Barack Obama's administration and a day before Donald Trump is to be inaugurated.
Two senior U.S. officials confirmed that Guzman was on his way.
One said the U.S. Drug Enforcement Administration took custody of Guzman in Ciudad Juarez, across the border from El Paso, Texas, and a plane carrying him departed for New York at 5:31 p.m. Eastern time. The officials agreed to give the information only if not quoted by name because they were not authorized to discuss the matter publicly.
New York is one of several U.S. jurisdictions where Guzman faces charges.
The convicted Sinaloa cartel boss has been held most recently in a prison near Ciudad Juarez. He was recaptured a year ago after escaping from a second maximum-security prison through a tunnel dug to his cell. He had fought extradition since then.
Associated Press writer Peter Orsi reported this story in Mexico City and AP writer Bradley Klapper reported from Washington.