Clarke's appointment was approved Monday by U.S. Magistrate Judge Marianne Bowler.
The judge denied, at least for now, a request from Miriam Conrad, the public defender of 19-year-old suspect Dzhokhar Tsarnaev, to appoint a second death penalty lawyer, David Bruck, a professor at Washington and Lee University School of Law.
Tsarnaev has been charged with using a weapon of mass destruction during the April 15 marathon. Three people were killed and more than 260 injured when two bombs exploded near the finish line.
The suspect's lawyers could renew their motion to appoint another death penalty expert if he is indicted, the judge said.
Tsarnaev's brother, 26-year-old Tamerlan Tsarnaev, also a suspect in the bombing, died after a gunbattle with police. Their mother has staunchly defended them, calling the bombing allegations against them lies.
Clarke's clients have included the Unabomber, Ted Kaczynski; Susan Smith, who drowned her two children; Atlanta Olympics bomber Eric Rudolph; and most recently Tucson, Ariz., shooter Jared Loughner. All received life sentences instead of the death penalty.
Clarke has rarely spoken publicly about her work and did not return a call seeking comment Monday. However, at a speech Friday at a legal conference in Los Angeles, she talked about how she had been "sucked into the black hole, the vortex" of death penalty cases 18 years ago when she represented Smith.
"I got a dose of understanding human behavior, and I learned what the death penalty does to us," she said. "I don't think it's a secret that I oppose the death penalty."
Harvard Law School professor Alan Dershowitz said the decision to put Clarke on Dzhokhar Tsarnaev's defense team shows "they are going to litigate hard against the death penalty."
"They are not going to put on a jihadi defense," he said. "The client wants to live, and he wants to avoid the death penalty. They are not going to say, 'I want to die, I want to join my brother.' "
Bruck has directed Washington and Lee's death penalty defense clinic, the Virginia Capital Case Clearinghouse, since 2004.
In other developments in the Boston case:
— FBI agents visited the Rhode Island home of Tamerlan Tsarnaev's in-laws and carried away several bags, at least one labeled as DNA samples, CNN reported.
Katherine Russell, Tsarnaev's widow, has been staying at the North Kingstown home and did not speak to reporters as she left her attorneys' office in Providence later in the day. Attorney Amato DeLuca says she's doing everything she can to assist with the investigation.
— President Barack Obama and Russian President Vladimir Putin discussed terrorism coordination Monday. Obama expressed his "appreciation" for Russia's close cooperation after the Boston Marathon attack.
The bombing suspects are Russian natives who moved to the Boston area. Russian authorities told U.S. officials before the bombings they had concerns about the family but only revealed details of wiretapped conversations since the attack.
— A medical examiner has determined but did not release the cause of death for Tamerlan Tsarnaev, authorities said. His body is unclaimed, and authorities said the information will remain private until his remains are released and a death certificate is filed.
Police have said he ran out of ammunition during the gunbattle before his brother dragged his body under a vehicle while fleeing.
AP Special Correspondent Linda Deutsch in Los Angeles contributed to this report.
This program aired on April 30, 2013. The audio for this program is not available.