Bishop O'Malley set a humble tone as he looked at the job ahead of him.
"The path has never been easy but today it seems overwhelming," he said at a news conference. "Still, I feel privileged to be called."
Bishop O'Malley, 59, succeeds Cardinal Bernard Law, who resigned in December amid public outrage that made it impossible for him to do his job.
Waves of molestation cases exposed a Roman Catholic hierarchy that sought to shield abusive priests rather than kick them out of parishes.
About 500 lawsuits have been filed against the archdiocese, with settlement negotiations so far failing to resolve them.
O'Malley, who won praise for cracking down on sex abuse in two other assignments hit by scandal - Massachusetts's Fall River and Palm Beach, Florida renewed the promise to settle the lawsuits.
Even if it's not a legal obligation, he said, there remains a moral obligation: "We must step up to the plate. People's lives are more important than money," Bishop O'Malley said.
The Vatican announced Bishop O'Malley's appointment in its daily bulletin. It also named his successor in Palm Beach, Bishop Gerald Barbarito, currently bishop of Ogdensburg, New York.
As word emerged that the Franciscan would be tapped for the Boston job, lawyers for victims praised Bishop O'Malley for his handling of the scandal, although other victims' groups urged caution.
Bishop O'Malley was sent in to Fall River to clean up a crisis in the early 1990s when the Rev James Porter was accused of molesting children.
Rev Porter ultimately pleaded guilty to molesting 28 children and was sentenced to 18 to 20 years in prison.
The diocese paid for treatment and medication for Rev Porter's victims.
"There could never be a better person in the country to have this job and to try to bring about real healing in the Archdiocese of Boston," said attorney Roderick MacLeish, who represented 101 of Rev Porter's victims and is also one of the lead lawyers for hundreds of plaintiffs with cases against the archdiocese.
The lay victims group Survivors Network of those Abused by Priests said it welcomed Bishop O'Malley and would work with him, but stressed that "no one person can magically undo the horrific pain so many in this archdiocese feel."
"He did lead the Fall River diocese in the aftermath of serial predator priest James Porter. But one case does not make a track record," said Ann Hagen Webb, New England coordinator of the group.
One of Rev Porter's victims said he hadn't been satisfied with his dealings with Bishop O'Malley.
"He's slick. He's good public relations. But as far as deep inside, he's not really going to solve the problem," said Frank Fitzpatrick.
"The reason is, he's just there to quiet things down."