US Attorney General Eric Holder said in a statement: "The nature of the conduct at issue and the resultant harm compel this decision."
Seventeen of 30 charges against the 20-year-old carry the possibility of capital punishment, including using a weapon of mass destruction to kill.
The bombings killed three and injured more than 260 in April 2013.
Mr Tsarnaev has pleaded not guilty and no trial date has been set.
Prosecutors allege that Mr Tsarnaev and his deceased older brother, Tamerlan Tsarnaev, built and planted two pressure cooker bombs near the finish line of the marathon.
The brothers lived in the Massachusetts town of Cambridge, home of the prestigious Harvard University, after emigrating to the US in 2002 from the Caucasus region of southern Russia.
Officials believe they set off the bombs in retaliation against the US for its military action in Muslim countries.
Tamerlan Tsarnaev was killed during a shootout with police days after the bombing. The younger brother was wounded and was eventually found inside a boat in a residential neighbourhood.
Prosecutors allege Mr Tsarnaev wrote about his motivation for the bombing on the inside of the boat.
He allegedly wrote the US government was killing "our innocent civilians" and "I can't stand to see such evil go unpunished".
Mr Tsarnaev is also charged with killing a university police officer and carjacking.
He will be charged under the federal death penalty law; Massachusetts abolished the use of capital punishment in 1984.
Since the federal death penalty was reinstated in 1988, 70 people convicted have been placed on death row.
But only three people have actually been executed, including Oklahoma City bomber Timothy McVeigh in 2001.
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