Ex-nun Nora Wall, 51, was convicted by a jury of eight men and four women at Dublin's Central Criminal Court late on Thursday night, with co-accused Paul "Pablo" McCabe, 50.
The former nun took part in the rape of a young girl, who was aged 10 at the time, at the state-funded St Michael's Child Care Centre at Cappoquin, County Waterford, in Ireland where she was the director.
Dublin's Central Criminal Court heard that Wall, the girl's guardian, held her by the ankles while McCabe, described as "a smelly vagabond" and a diagnosed schizophrenic, raped her in her bedroom between January 1987 and December 1989.
Another resident at the home, now aged 26, witnessed the rape. She said she opened the bedroom door, saw the two accused, and shouted "What the hell is going on?"
The victim alleged that there had been a second attack close to her 12th birthday.
Wall, known as Sister Dominic, was also found guilty of indecently assaulting the girl, now aged 21. She and McCabe were acquitted of raping the girl on the second occasion after conflicting evidence over dates.
Wall became director at Cappoquin in 1978. The home, housing up to 30 children, aimed to provide more family-type accommodation in place of a more austere "industrial school" at the same site, where McCabe grew up in the 1950s. He met Wall around 1980 when he returned in an effort to trace his mother.
McCabe said he visited the centre regularly in the 1980s. He revealed Wall had said he was "like St Augustine" when he told her of molesting the girl, and said "only God knows what is wrong" when he told her he thought he had done wrong.
Wall claimed she had never had any sexual contacts with any of the young people in her care. She alleged the girl was known for making up stories and at one stage had claimed she was sexually abused by her own father. "Nothing was beyond her. Wherever there was trouble she was sure to be there," she said.
McCabe said in evidence he had made up his confession while under pressure during interrogation. He alleged he had not received adequate treatment for his schizophrenia while questioned and had neglected to take his medication over a number of weeks previously.
Wall and McCabe were remanded on bail for sentencing on 23 July.
A spokeswoman for the Sisters of Mercy said they were "devastated by the revolting crimes", urging anyone abused while in their care to contact the police. She added: "Our hearts and prayers go out to this young woman, who was entrusted to us as a child. Her courage in coming forward was and is heroic.
"We beg anyone who may have been abused in our care to come forward. We would also ask for prayers for everyone touched by these events."
Wall departed from the home in 1992, with health authority references saying her professional abilities were "of the highest calibre", and left the Order in 1994. She later worked in a hostel in Dublin for women and children and in a Romanian orphanage.