The Los Angeles Police Department's Internet Crimes Against Children unit learned that Jose Rosario Alvarez had been involved with the girl over the Internet and in person-to-person contact.
Alvarez, 27, faces charges of having unlawful sex with a minor, who attends another Los Angeles Unified school.
The school district has removed Alvarez from contact with students pending further proceedings.
Anyone with information on the case was asked to call detectives at (213) 486-0570.
City News Service contributed to this story.