The actor was arrested in New York on Monday.
Prosecutors said Miller called in a fake alert on 18 March after getting into an argument with a woman on the train travelling from Washington DC to New York.
“I am worried for everyone on that train,” Miller allegedly told police. “Someone has to check that lady out.”
The train was stopped in Westport, Connecticut, but no explosives were found during a search.
Miller was released on a $100,000 (£70,300) bail after an initial appearance in federal court in New Haven on Tuesday.
He faces up to five years in prison if convicted.
The 36-year-old played Erlich Bachman in HBO’s Silicon Valley from 2014 to 2017 and has also had starring roles in films such as Cloverfield and Deadpool.