The charges came about after a 26-year-old man reportedly encouraged by last year's trial of Msgr. William J. Lynn - the first Catholic church official convicted for a supervisory role in covering up the conduct of pedophile priests - contacted archdiocesan officials in January.
That same day, Williams said, church officials called his office and relayed the man's allegation: Brennan sexually abused him from ages 11 to 14, within the statute of limitations.
Williams said Brennan was arrested late Wednesday at the private home in Perryville, Md., where he has lived for much of the last eight years.
Brennan was being held Thursday in Cecil County, Md., awaiting extradition to Philadelphia. When he returns, he will be charged with rape, involuntary deviate sexual intercourse, and aggravated indecent assault, Williams said.
"A serial sexual abuser is now behind bars thanks to the brave actions of this young man," Williams said.
Brennan's arrest is the second of a priest triggered by the Lynn verdict.
In July 2012, three days after Lynn's sentencing, Williams announced the arrest of the Rev. Andrew McCormick on charges of sexually assaulting a 10-year-old altar boy at St. John Cantius parish in Bridesburg. McCormick, 57, of Pottstown, is scheduled to go on trial Feb. 24.
Williams commended church leaders for immediately reporting the new allegation. He said he hopes the arrest "continues to send a message to sexual-assault victims that we hear you and we will bring the person or people responsible for your unimaginable pain to justice."
Archdiocesan officials cited Brennan's arrest as evidence of Archbishop Charles J. Chaput's "strong commitment to work with law enforcement in ensuring justice for victims of sexual assault."
SNAP, the Survivors Network of those Abused by Priests, praised the arrest but urged caution.
"We are disappointed that Catholic officials are being praised for simply, finally, obeying the law," said SNAP national director David Clohessy. "We caution Mr. Williams and Philadelphia Catholics against premature complacency."
Though Brennan was not charged after the 2005 or 2011 grand jury reports on priest sex abuse, prosecutors made him a large part of the Lynn trial.
Prosecutors introduced details of Brennan's history and about 20 others to show Lynn and church leaders had a long-standing practice of moving abusive priests to different parishes, where they found new victims. As secretary of clergy from 1992 to 2004, Lynn was responsible for investigating misconduct complaints against priests and recommending action to the archbishop.
Lynn, 62, was convicted of one count of child endangerment and is serving a 3- to 6-year prison term in Waymart state prison in Northeast Pennsylvania.
According to trial testimony, Brennan, who was ordained in 1964, engaged in inappropriate or suspicious behavior with more than 20 boys from 1988 to 2004 at parishes in Philadelphia, Bucks, and Montgomery Counties.
Archdiocesan officials had Brennan undergo several psychological evaluations, which concluded that he was a likely pedophile who would abuse other children. Brennan, however, was shipped from one parish to another, told to "keep a low profile" but not barred from contact with young people.
Williams called Brennan "another example of how Msgr. William Lynn shielded predator priests from exposure and prosecution and led to the victimization of countless Philadelphia-area children."
The 2005 grand jury report said complaints about Brennan's behavior with young boys and teens began shortly after then-Cardinal Anthony J. Bevilacqua appointed him pastor of St. Ignatius parish in Yardley, Bucks County, in 1988.
Six months after Brennan's arrival, Bevilacqua sent him to St. John Vianney, the church-owned Downingtown hospital for clergy with sexual, emotional, and substance-abuse problems. His Yardley parishioners were told he was "on a retreat."
In 1989, Brennan was appointed administrator and then pastor of St. Mary's parish in Schwenksville, Montgomery County. Within months, there were complaints and Brennan went back to St. John Vianney in 1992. According to the grand jury, experts recommended he not be assigned to a new parish without a "ministry supervision team" to closely monitor his activities.
Nevertheless, Brennan was named assistant pastor at Resurrection of Our Lord in 1993 without a supervision in place. And it was there that he allegedly assaulted the altar boy between 1998 and 2001 in the church sacristy, the rectory, a parish storage area, and a movie theater.
Bevilacqua testified before the grand jury that he considered Brennan's problems "innocuous-sounding boundary issues."
Assistant District Attorney Evangelia Manos said that after Brennan's name appeared in the 2005 grand jury report, he relocated to Maryland under church orders not to perform any canonical duties.
He remains an ordained priest although the church has begun the process that could result in his being defrocked, Manos said.