The United States have been handed a massive drug case with the extradition of El Chapo.
Guzman is the head of the Sinaloa cartel, which is accused of generating much of the deadly violence in Mexico and providing tons of drugs to the United States.
He had been fighting his extradition ever since he was recaptured almost exactly a year ago in his home state of Sinaloa.
The Mexican government "delivered Mr. Guzman Loera to the authorities of the United States" after the Supreme Court and a court of appeals rejected his latest bids to avoid extradition, the foreign ministry said in a statement.
The appeals court ruled that the extradition conformed with a bilateral treaty and that Guzman's rights had not been violated, the statement said.
The government did not say to which state Guzman was sent. CNN and ABC News reported that Guzman was headed to New York.
A US government official, who spoke on condition of anonymity, would only confirm to AFP that Guzman was already on US soil.
In May, the Mexican foreign ministry approved extradition bids from California, where he is wanted for drug distribution, and Texas, where he faces a slew of charges including murder and money laundering.
Trump, who takes office on Friday, has publicly clashed with Mexico over trade and immigration issues. The Republican president-in-waiting has pledged to build a wall on the US-Mexican border.