The Honduran government announced the move, saying Hernández was being taken to New York.
He was placed in a US Drug Enforcement Administration plane that took off from Toncontin International Airport at around 4:20 p.m. local time, Honduran authorities said.
Hernández’s wife, Ana Garcia, posted a video of the former president on her Twitter account.
“The truth is a liberating force when it’s revealed, it’s my prayer, my family’s and of thousands of Honduran families, so the truth is revealed and prevails in my case. I am innocent, I have been, and I am unfairly treated by the process,” he said.
“You know that I worked tirelessly to restore peace in Honduras. We gave our maximum effort for our nation, and it’s unfortunate that those who turned Honduras into one of the most violent countries on Earth, those villains, now want to be heroes,” Hernández said in the video, whose recording date is unknown.
The Honduran Supreme Court said in a statement that it voted unanimously in favor of extradition on the first charge “regarding importing a controlled substance to the United States.” A majority voted to extradite him on two charges related to firearms possession.
Hernández left office in January after eight years as president.
Hernández’s brother, Tony Hernández, is currently serving a life sentence in a US federal prison for drug trafficking.
According to court filings in that case, US authorities believe Hernández was a co-conspirator in the operation, funneling drug money to help fund his presidential campaigns. Hernández has repeatedly denied those allegations.
CNN’s Stefano Pozzebon, Valentina Di Donato and Harmeet Kaur contributed to this report. Elvin Sandoval reported from Tegucigalpa, Honduras