Pictures show how Juan Orlando Hernández, handcuffed and surrounded by an extensive police force, boarded a helicopter in Honduras' capital Tegucigalpa and on to the airport.
There, further travel to the United States awaited together with agents from the American drug police DEA, reports the news agency AP.
Hernández took office as president in 2014 and served as president until January this year, when Xiomara Castro was sworn in as the country's first female president.
Hernández's time in power was marked by suspicions of corruption and accusations that he was turning the country into a dictatorship.
At the same time, the country's drug cartels gained more influence during his time as president.
According to the AP, Hernández was arrested at his residence in Tegucigalpa in February - at the request of US authorities.
Following Honduran's Supreme Court ruling rejecting an appeal by Hernández, the extradition has now been executed.
In the US, Hernández will be brought to justice in New York on suspicion of gun crime and for smuggling drugs to the US, writes AP.
Defense speech: "Being unfairly prosecuted"
Hernández denies any wrongdoing and says he is exposed to false testimonies from drug lords who he says want revenge.
In a video that Hernández's wife published on social media on Thursday, Hernández says he is innocent.
"I have been and am being unfairly prosecuted."
"You all know that I have worked tirelessly to restore peace in Honduras," Hernández said in the video.
"El Chapo" must have funded election campaigns
Just over a year ago, the ex-president's brother Tony Hernández was sentenced to life in prison in the United States for drug smuggling.
Bribes he received from the now life-sentenced drug king Joaquín "El Chapo" Guzmán are said to have gone to several of his brother Juan Orlando's election campaigns.
Hernández has also previously denied any knowledge of the drug money and has instead said that he worked to fight the drug trade in Honduras and that he is allied with the United States against the cartels.