Father Michael Higginbottom, 74, is accused of abusing the boy while he was a teacher at St Joseph's College in Upholland, Lancashire, in the 1970s.
It was a venue for "mental, physical and sexual abuse', Liverpool Crown Court was told.
He denies four counts of a serious sexual offence and indecent assault.
The boy was aged between 13 and 14 at the time of the alleged abuse.
The court heard Mr Higginbottom, now of West Farm Road, Newcastle, said he would strike the alleged victim with a strap if he did not attend his living quarters, where much of the abuse was alleged to have happened, at appointed times.
The boarding school, which has now closed, was attended by boys aged 11 to 18, many of whom were considering a career in the priesthood.
David Temkin, prosecuting, said the boy described the school as a "cold, dark and forbidding place".
He added: "He told the police that for him it was the venue for 'mental, physical and sexual abuse'."
Mr Temkin said the defendant worked at the school as a priest and teacher and was "therefore in a position of trust".
The court was told that about a week after the boy started at the college, he was invited into Mr Higginbottom's living quarters where he locked the door and ordered him to undress before sexually assaulting him.
Mr Temkin said the defendant then told the boy things would "get easier" for him at the college.
The victim revealed the allegations to a friend in 2013, who encouraged him to report them to police.
When Higginbottom was arrested he told the police the claims were "total lies" and could not remember the complainant.
The trial continues.
A Catholic priest who sexually abused a teenage student breached his position of trust in a "spectacular and horrific" way, a court has heard.