Joseph Boeckmann resigned in May after dozens of men claimed he paid them to allow him to spank them with a paddle and to take photos of the red skin.
Mr Boeckmann, 70, has previously denied the allegations through his lawyer.
According to a federal indictment, he now faces 21 separate charges.
They include eight counts of wire fraud, two counts of witness tampering, one count of federal programme bribery and 10 counts of violating the federal Travel Act.
'Among the worst'
The indictment accuses Mr Boeckmann of "corruptly using his official position as an Arkansas district judge to obtain personal services, sexual contact, and the opportunity to view and to photograph in compromising positions persons who appeared before him in traffic and misdemeanour criminal cases in exchange for dismissing the cases".
At least one of his alleged victims was only 16, the indictment states.
It has also been alleged the former Cross County District Court judge also allegedly had more than 4,600 photos of nude or semi-nude men on his computer.
Mr Boeckmann resigned earlier this year after an investigation into allegations of inappropriate sexual relationships with men accused of crimes dating back to his time as a prosecutor decades earlier.
The head of the Arkansas Judicial Discipline and Disability Commission, which conducted the initial investigation, has called the allegations "if not the worst, among the worst cases of judicial misconduct'' in state history.