The man, who was 13 when he attended St William's in Market Weighton, told the jury James Carragher used to make him "upset" before he was abused.
The ex-principal denies 50 counts of indecent assault between the 1970s at the East Riding of Yorkshire site.
At Leeds Crown Court, Mr Carragher also denies 12 other serious sex offences.
Earlier in the trial, the jury heard the 75-year-old, of Merseyside, was jailed for seven years in 1993 and 14 years in 2004 for sex offences.
The home for boys with behavioural problems was run by the De La Salle order. It has since closed.
Giving evidence behind a screen for legal reasons, the former pupil said he was sexually abused by Mr Carragher on "a number of occasions".
"He would get me upset to get me to start crying. He put his arm around me trying to comfort me and would then start touching me," he said.
Richard Wright QC, prosecuting, asked: "Why did you not go to the police sooner?"
He replied: "I was ashamed. Even though I was only a child, I still let him do it."
The man said he had not discussed the matter for 45 years.
Mr Carragher is on trial along with former chaplain at St William's, Anthony McCallen, 69, and former teacher Michael Curran, 62.
The jury was previously told how Mr McCallen was convicted of abusing two boys in the 1990s.
Mr Curran has no previous convictions.
Mr McCallen, of Merseyside, denies 18 indecent assaults and seven other serious sexual offences.
Mr Curran, of Teesside, denies one count of assault occasioning actual bodily harm and another of indecent assault.
The trial continues.
A former pupil at a Catholic home and school for delinquent boys told a court he could not report his alleged abuser to police because he felt "ashamed".