Timothy Morris, 29, of Seaford, was arrested this week.
Police say the investigation began in May, 2012, when detectives were contacted a relative of one of the victims, who is now 19 years old, to say the teen was involved in a sexual relationship with an adult employee of the Sussex Technical High School when she was 16.
Investigators say they were able to determine the relationship took place, but said the victim did not want to proceed with the investigation.
Then, on Wednesday, police say they were contacted by Sussex Technical High School officials after a current 16-year-old student told them she was being sexually harassed.
The teen told police that Morris would give her unsolicited hugs and, in once incident, tried to kiss her, making her feel "uncomfortable" and "scared." Police say Morris also obtained the victim's cell phone number through social media and began to send her text messages.
On Thursday, the 19-year-old victim was again contacted by police. Investigators say she confirmed the sexual relationship with Morris, which began in March, 2010, when she was 16. She said the two would have sex both inside and outside of school.
The relationship continued for a year and a half, police said, before ending in August, 2011.
Morris was charged with 25 counts of Rape by a Person in Position of Trust, Authority, or Supervision, 25 counts of Unlawful Sexual Contact, Continuous Sexual Abuse of a Child, and Sexual Harassment.
He is being held on $208,500 cash bail.
There was no immediate word on Morris' employment status with the school.