Monsignor William Lynn was found guilty on one count of child endangerment, but not guilty on another count of child endangerment and not guilty on one count of conspiracy.
The jury said it was hung on the two charges for the Rev. James Brennan.
The struggling jury in Philadelphia had returned to court to deliberate on Friday morning.
Jurors were ordered back to work after telling a judge they were deadlocked on four of five charges on Wednesday.
The jury had a day off on Thursday.
Friday marked the 13th day of deliberations.
Seven men and five women sat on the jury, along with eight alternates. Many have ties to Catholic schools or parishes, but said they could judge the case fairly.
There are about 1.5 million Catholics in the five-county archdiocese.
