The US Marshals Service said the 19-year-old had been moved from the Beth Israel Deaconess Medical Center to a facility at Fort Devens, Massachusetts.
Dzhokhar Tsarnaev has been in hospital since his arrest following a huge police operation a week ago.
He was found badly injured in a boat in a suburban backyard. His brother, Tamerlan Tsarnaev was killed during the manhunt.
Many of the injured have also been treated at the Beth Israel Deaconess Medical Center, and were reported to be unhappy at having the surviving bombing suspect in the same building.
The US Marshals Service said the accused, whose condition has been described as fair, was taken overnight to the Federal Medical Center Devens some 40 miles west of Boston.
The facility, on the decommissioned Fort Devens US Army base, treats federal prisoners and detainees who require specialized long-term medical or mental health care, the Associated Press reports.
Dzhokhar Tsarnaev was charged, by a magistrate at his hospital bedside earlier this week, with using a weapon of mass destruction and malicious destruction of property resulting in death.
He could be sentenced to death if convicted on either count.
Having suffered apparent gunshot wounds to the head, neck, legs and hand, he was reported to have responded to questions in writing because a throat wound left him unable to speak.
The two bombs, placed in pressure cookers and left close to the finishing line of the Boston Marathon on April 15, killed three people and wounded more than 260.
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