The move, which will increase tensions between the two nations, was announced by Attorney General William Barr.
It has long accused him of leading a corrupt and brutal regime, a charge he has repeatedly rejected.
Washington backs opposition leader Juan Guaidó, who last year declared himself interim president.
As well as Mr Maduro, the US indictment also charged four other senior Venezuelan officials including the country’s chief justice.
“The Venezuelan people deserve a transparent, responsible, representative government that serves the needs of the people – and that does not…. engage in illicit narcotics trafficking,” the US State Department said in a statement.
“These individuals violated the public trust by facilitating shipments of narcotics from Venezuela, including control over planes that leave from a Venezuelan air base,” it added.