Michael Curran, 62, went on trial at Leeds Crown Court last month accused of assault occasioning actual bodily harm and indecent assault.
Judge Geoffrey Marson QC directed the jury to return not guilty verdicts on both charges.
The jury had heard that Mr Curran was a teacher at St William’s residential home and school for boys with behavioural problems, in Market Weighton, East Yorkshire.
He was on trial with former principal James Carragher, 75, and 69-year-old former chaplain Anthony McCallen, who each deny charges of indecent assault and serious sexual offences against boys at the school, which was run by the Catholic De La Salle order.
The trial continues.