Civil liberties groups reacted angrily to the news that Dzhokhar Tsarnaev, 20, is to be put to death if a jury finds him guilty at his trial.
Three people died and 264 people were injured in the attacks on one of America's biggest running events last April. It was one of the largest terror attack on US soil since September 11, 2001.
Attorney General Eric Holder said he would authorise trial prosecutors to seek the death penalty against Tsarnaev.
Mr Holder, who made the decision hours before today's deadline, said: "The nature of the conduct at issue and the resultant harm compel this decision."
Seventeen of 30 charges against Tsarnaev carry the possibility of the death penalty, including using a weapon of mass destruction to kill. The 20-year-old has pleaded not guilty. No trial date has been set.
The American Civil Liberties Union of Massachusetts pointed out the trial would go ahead in a state that had scrapped the death penalty decades ago.
"I wish Federal officials would have respected the clear wishes of the people of Massachusetts, who were on the front lines in this tragic event," said executive director Carol Rose.
It follows a newspaper poll last year that found 57% of Boston residents favoured life in prison for Tsarnaev, if he is convicted, with 33% in favour of his execution.
Prosecutors say Tsarnaev, and his brother Tamerlan, 26, planted a pair of homemade pressure-cooker bombs at the race's crowded finish line. The dead included an eight-year-old boy.
It is alleged the brothers later killed a university police officer and later engaged in a shootout with police that left Tamerlan dead.