Mejia is now on administrative leave while he faces felony charges. Prosecutors allege that the sexual acts took place in his office at the school before, during and after classes over a four-month period, beginning in December 2008.
Mejia has worked for the school for 12 years.
Prosecutors allege the janitor groomed his victim, offering the special-education student gifts, money and candy.
"In addition to the number of cards and gifts that were exchanged, they had exchanged hundreds of text messages and phone calls between the two of them over a several month period as well," said prosecutor Robert Mestman.
"He would usually close the door. Several times he'd have someone tape over the surveillance cameras. Other times he'd have employees stand watch outside to alert him if any other people or his wife would show up on campus unexpected," Mestman said.
Prosecutors say the other employees who stood watch were not aware of the alleged abuse, and are not facing charges.
Authorities became aware of the allegations last month after the victim's friends went to the school principal.
"I think it's very disturbing knowing that we go to the same school with him, and he's like the janitor and walks around," said student Jessica Pelayo.
Luis Mejia faces a maximum of 12 years and eight months in prison if convicted.
Police say that Mejia allegedly tricked the other employees who stood watch outside the janitor's office.
In the case of the employee who covered up the security camera with tape, he was told, according to police, there was going to be painting done and the camera had to be protected from any paint.
The school district says that it is going to take a closer look at the police report once they receive it and then they'll go from there. They'll decide if those employees should face any disciplinary.
"It's really wrong because the girl didn't know what to expect because she' s disabled, and it's sort of disturbing because he has the keys and can do anything in any room," said student Sonia Cortez.
At least two other employees at El Modena High School have faced misconduct investigations since 2007, when the principal, Brent Bailey, resigned, accused of trying to engage in lewd acts at a park in Fullerton. Bailey pleaded guilty the same year.
Last year, Carlie Attebury, a music teacher at the school, was arrested, accused of having sex with a male student, starting when he was 15. Attebury plead not guilty to the charges.