The Merced Police Department says the investigation began on Tuesday following a report from the Merced Union High School District.
Detectives identified 34-year-old John Mobley III as the suspect.
He has been employed as an Intervention Coordinator at El Capitan High School since August 2024.
Police took him into custody and booked him into Merced County Jail on several charges including statutory rape.
The Merced Union High School District released a statement about the arrest, writing:
"As soon as Administration became aware of reports that John Mobley III had engaged in inappropriate conduct with a student, he was immediately placed on administrative leave."
The district is also conducting its own investigation.
Anyone with information on this case is urged to contact the Merced Police Department.