The jury had deliberated the charges against the Rev. Andrew McCormick for more than four days. The 26-year-old accuser testified he was sexually assaulted in a rectory bedroom by the priest in 1997, allegations that McCormick denies.
Prosecutors plan to retry McCormick, who has been suspended from the church since 2011 over complaints about his behavior around children. He remains free on bail and is due back in court on April 28. A gag order remains in effect.
On the witness stand last month, the accuser said he had repeatedly tried to hang himself after the alleged assault, starting at age 11. His mother had gone to the priest a year earlier with concerns that her son was gay.
"I couldn't deal with the guilt of what had happened, or what I am," he said.
He told a cousin early on that he had been molested, and later told classmates on a high school retreat. However, he did not share the details, most notably that the alleged assailant was a priest. Both the cousin and a classmate confirmed the disclosures when they testified.
However, McCormick had witnesses of his own to support his version of events. They included two young men who had gone to Poland as boys with McCormick, and said they were not abused. McCormick paid at least some of their way.
The attack allegedly occurred at St. John Cantius, a large Polish parish in northeast Philadelphia, where McCormick was stationed from 1986 to 2000.
Afterward, the priest taunted the altar boy, warning that homosexuality was a sin, he said.
"If it's a sin, it means I'm going to hell," he remembered thinking.
The Associated Press does not typically identify people who say they are the victims of sexual assault without their consent.
A small but loyal group of parishioners from St. John Cantius attended the trial to support McCormick, who was charged with counts including sexual assault and corruption of minors.
Defense lawyers questioned why only one person had accused McCormick of sexual assault, especially after publicity about his arrest in 2012.
Defense attorney William J. Brennan asked jurors not to pre-judge McCormick because of other abuse cases involving priests.
Philadelphia prosecutors have been investigating priest-abuse reports for more than a decade and have won several convictions. The most notable case, the child-endangerment conviction of Monsignor William Lynn, who long handled abuse complaints for the archdiocese, was recently thrown out on appeal. However, prosecutors have asked the state Supreme Court to reinstate it.