The 29-year-old was arrested at his home at Bradbury, near Campbelltown, on Thursday morning by detectives from the child abuse squad.
The investigation began last week after police received a report that an 11-year-old boy had been indecently assaulted by a teacher.
The teacher has been charged with ten counts of indecently assaulting a person under 16, three counts of child grooming and an aggravated act of indecency.
Police will allege that the teacher groomed and then indecently assaulted the boys at the school, which cannot be named for legal reasons, between 2012 and 2015. He has been refused bail and will appear in Campbelltown Local Court on Friday.