According to a police report, officials were alerted to a break-in on 1 May in the town of Stamford.
Surveillance video led them to suspect the actor, who stars in films including the Fantastic Beasts franchise.
Miller is separately facing charges of assault in Hawaii and allegations of abuse from several women.
Vermont State Police said there was no-one at home when the house was broken into.
"As a result of an investigation that included surveillance videos and statements, probable cause was found to charge Ezra M Miller with the offence of felony burglary into an unoccupied dwelling," police said in a statement on Monday.
The Justice League actor was ordered to appear in court to face the charge on 26 September.
The alleged burglary is the latest in a string of incidents involving the 29-year-old actor.
In April, Hawaii police arrested Miller for allegedly throwing a chair, which then hit a 26-year-old woman on the forehead.
Just two weeks earlier, Miller was charged with harassment and disorderly conduct at a karaoke bar in Hawaii.
According to police, the actor grabbed a microphone from a woman singing and lunged at a man playing darts after becoming aggravated by a rendition of Shallow from the film A Star Is Born.
Miller, who uses "they" and "them" as personal pronouns, is known for their roles in Perks of Being a Wallflower, Trainwreck and the hugely successful Fantastic Beasts franchise.
They are due to star as Flash in DC's upcoming film The Flash, set to be released next year.