Mr McClean, an English and drama teacher who also coached rugby, worked at the prestigious south Dublin school for decades.
John McClean (77) is charged with more than 40 counts of indecently assaulting the boys over an 18 year period between 1972 and 1990.
He is facing a jury trial in the circuit court after the Director of Public Prosecution (DPP) ruled that the allegations were too serious for the district court.
Judge John King remanded him on bail to a date in October to facilitate the preparation of a book of evidence.
The accused, with an address at Casimir Avenue, Harold's Cross, Dublin 6, is facing 49 counts of indecent assault on dates between 1972 and 1990.
The offences allegedly took place at Terenure College, Templeogue Road, Terenure, where Mr McClean was an English teacher and rugby coach.
Garda James Duffy told Dublin District Court that he arrested and charged Mr McClean before the court.
He was handed a true copy of each charge sheet and he made no reply after caution.
Defence solicitor Dara Robinson said there was no application for legal aid at this stage.
Wearing a navy blazer and black trousers, Mr McClean sat facing the judge and holding his hand to the side of his face.
He did not address the court during the brief hearing.
The accused has not yet indicated how he intends pleading to the charges.
Mr McClean, an English and drama teacher who also coached rugby, worked at the prestigious south Dublin school for decades before taking up a rugby coaching position in UCD in the 1990s.