Carlos Arnoldo Lobo, also known as "Negro Lobo", or black wolf, was arrested in the Central American country in late March. He is wanted by US authorities on drug trafficking charges.
State Department spokeswoman Jen Psaki said the 38-year-old's extradition took place Thursday, confirming an earlier announcement by President Juan Orlando Hernandez.
"We commend Honduras' resolve in taking this historic step to extradite one of its own citizens, which strikes a blow against impunity for organized crime and narcotics trafficking," she said in a statement.
In 2012, the Honduran Congress approved a constitutional reform allowing the extradition of Honduran suspects for drug trafficking and terrorism. Until then, only foreigners could be extradited.
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Lobo's extradition is a first such case of a Honduran national.
"The government of Honduras, including its Supreme Court, has sent a clear message that those accused of crimes that jeopardize the safety of Honduran citizens will not be allowed to hide from justice," Psaki said.
It has led to an epidemic of violence in the region's poor countries like Honduras, which has the world's highest murder rate as gangs fight over drug trafficking routes.
"The United States fully supports Honduran efforts to strengthen the rule of law and improve the quality of life for all Hondurans," Psaki said.