Maurice Blackwell, 58, who did not testify, molested Dontee Stokes, 29, when Blackwell was pastor of St. Edward, a Roman Catholic church in West Baltimore. Stokes said the molestation began when he was 13 and continued until he was 17.
Blackwell is scheduled to be sentenced April 15.
The jury convicted Blackwell of abusing Stokes of 1990, 1991 and 1992 but acquitted him of the charge relating to Stokes' allegation that the abuse began in 1989.
The jury deliberated 5½ hours over two days.
In their closing arguments Wednesday, Blackwell's attorney portrayed Stokes as a disturbed young man who made up the allegations to deal with a sexual identity crisis, while the prosecution called him a vulnerable victim preyed upon by a trusted father figure.
Defense attorney Kenneth Ravenell told jurors Stokes had homosexual tendencies and was "willing to lie" to protect the secret of his sexual orientation.
"There was absolutely no credibility to anything Dontee Stokes has told you," he said.
Stokes acknowledged in court that he has had trouble distinguishing between fantasy and reality at times, but maintained he was sexually abused in Blackwell's rectory.
Prosecutor Jo Anne Stanton called the allegations that Stokes was concealing homosexual tendencies a "smoke screen."
Stokes shot and wounded the former priest three years ago. He was acquitted of attempted murder in December 2002 but was convicted on gun charges. He served 18 months on home detention.
Blackwell was stripped of his church authority after acknowledging he had a sexual relationship with a teenage boy in the early 1970s. The Vatican defrocked him in October.