Dzhokhar Tsarnaev, 19, who was charged in hospital, could face the death penalty.
A White House spokesman has said Dzhokhar Tsarnaev will not be treated as an “enemy combatant”, as suggested by some Republican members of Congress.
The twin bomb attack near the Boston Marathon finishing line killed three people, and injured more than 180.
Dzhokhar Tsarnaev was captured on Friday evening after a huge manhunt during which his older brother and suspected fellow bomber, Tamerlan Tsarnaev, died.
He has been unable to speak because of a throat wound, though he has reportedly responded to questions in writing.
As well as a count of using a weapon of mass destruction, Dzhokhar Tsarnaev faces one count of malicious destruction of property resulting in death, the Department of Justice said in a statement.
In addition to federal charges, prosecutors for the state of Massachusetts, which does not have the death penalty, could file their own.
“He will not be treated as an enemy combatant,” said White House spokesman Jay Carney.
“We will prosecute this terrorist through our civilian system of justice.”
The city of Boston is due to observe a moment of silence for the victims at 14:50 local time, exactly one week after the attack.
Also on Monday, a private funeral was being held for 29-year-old restaurant worker Krystle Campbell, who was killed at the marathon finish line after going to watch the race with a friend.
A memorial service was scheduled later for another victim, Lu Lingzi, a 23-year-old graduate student from China.
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