Thomas Black was head of biology at St Mungo’s Roman Catholic High School in Falkirk at the time of the alleged offences.
Black, now 70, faces two charges of indecently assaulting the boys, who were pupils at the school at the time.
It is alleged that on various occasions between January 1989 and December 1994, at the school, he touched and rubbed the body and private parts of one boy, then aged 15 to 17, through his clothing, and did the same to another boy, aged 14 to 17.
In the case of the second boy, it is alleged that he also indecently assaulted him while travelling in a car in Falkirk, and that he once removed the boy’s private parts from his clothing before committing a sexual act.
Both alleged victims are now men in their 40s.
At a procedural hearing at Stirling Sheriff Court today, Black, of Cardross Road, Dumbarton, pleaded not guilty to both charges against him.
The court was told it was a matter of agreement that Black was working at the school at the time as head of biology and the alleged victims were pupils at the establishment.
Sheriff Simon Collins continued the case to a further preliminary hearing on August 7, when it is hoped a trial date can be set.