The office that investigates misconduct at New York City schools said the assistant principal, William Abreu, raped a 17-year-old graduate in his office at Progress High School for Professional Careers in 2009.
Officials say Juan Martinez, a former after school employee at the school, forced a 16-year-old student to perform oral sex on him in 2011.
Both men were arrested and pleaded not guilty at their arraignments Wednesday.
An attorney for Abreu told the Daily News his client denies the charges. Martinez's lawyer said his client is innocent.
The indictments follow a report on the two educators by the Department of Education's Special Commissioner of Investigation.