Robel Phillipos, 19, was charged with two counts of making false statements to police during a probe into the April 15 attack that left three dead and scores injured.
The Cambridge student faces up to 16 years in jail if he is found guilty.
The indictment comes two weeks after two other friends of Tsarnaev pleaded not guilty to charges of impeding the investigation.
Dias Kadyrbayev and Azamat Tazhayakov, both 19-year-olds from Kazakhstan, face up to 20 years in prison and the prospect of deportation from the United States if convicted.
The indictment alleges that after the FBI released photographs of the suspects, Dzhokhar Tsarnaev sent Kadyrbayev a text message suggesting that he go to Tsarnaev's "room and take what's there."
The three young men then went to Tsarnaev's dormitory room and removed a laptop and a backpack containing fireworks and other items, prosecutors allege.
Later that night Kadyrbayev is accused of putting the backpack in a garbage bag and placing it in a dumpster outside their apartment.
Tamerlan Tsarnaev was killed during a shootout with police, while his younger brother -- who has pleaded not guilty to 30 counts, 17 of which are punishable by death -- was later arrested, wounded and hiding inside a small boat in a nearby backyard.
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