The abuse allegedly started in 1996, when Ayres was a seminarian, and continued through 1999, when he was ordained a priest, according to the complaint.
Ayres, 39, has been suspended from active ministry over a sex-abuse allegation from an unnamed accuser in November. He did not respond to a message left for him Wednesday at the Upper Darby home for clergy where he lives.
Donna Farrell, a spokeswoman for the archdiocese, declined to comment.
The lawsuit is at least the ninth in Philadelphia filed by an alleged clergy sex-abuse victim since February, when four current and former archdiocesan priests were arrested and a grand jury report criticized local church leaders for their handling of abuse complaints.
Unlike the previous lawsuits, this one involves allegations that appear to fall within the state's criminal statute of limitations, which was extended in 2002 to let victims of child sex abuse file complaints up to age 30. (It has since been extended further.)
Lawyers for the man say he has been cooperating with authorities.
"There is a criminal investigation going on that he's spoken to the D.A. about," said Daniel Monahan, one of his attorneys.
Tasha Jamerson, a spokeswoman for District Attorney Seth Williams, said the office would not confirm or discuss any pending investigations.
Marci Hamilton, a lawyer for the former Incarnation altar boy, said she was not sure whether his complaint or another had launched the investigation into Ayers.
According to the lawsuit, the complainant said he told the pastor at Incarnation last fall that Ayres had abused him, and the pastor allegedly replied that Ayres "was already under investigation and there had been reports filed before [his] abuse had occurred."
Ayres was a seminarian when he began serving in 1996 at Incarnation, on North Fifth Street near Fern Rock, according to the lawsuit and previous statements by the archdiocese. He remained at Incarnation until 2002.
He later served at St. Katharine Drexel parish in Chester as director of the Office for Pastoral Care of Migrants and Refugees, and as coordinator of the Laotian Apostolate. He was pastor of St. Michael's in North Philadelphia when he was asked to step down in 2010.
The lawsuit says the abuse had lasting impact on the former altar boy's life, hurting his job prospects and prompting him to seek medical and psychological treatment. His lawyers declined to elaborate.
The suit accuses the priest and church leaders of child sexual abuse, negligence, and conspiracy and seeks damages of at least $50,000.
Citing the grand jury report, the lawsuit says the archdiocese had a history of protecting sexually abusive priests and should have known that Ayres "had a sexual interest in children," although it doesn't say why.
Contact staff writer John P. Martin at 215-854-4774, firstname.lastname@example.org, or @JPMartinInky on Twitter.