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Mejia appeared to say a prayer before his arraignment, as he was surrounded by family members in the courtroom.
Orange County Superior Court Judge John Adams issued a protective order to keep Mejia away from the alleged victim. Prosecutors said that include all forms of contact.
Prosecutors said the alleged sexual acts took place in his office at the school before, during and after classes to a girl who is developmentally disabled.
Mejia, who has worked at the school for 12 years, allegedly gained the girl's trust by giving her candy, gifts and writing her cards and "I love you" notes.
Prosecutors said the two exchanged hundreds of text messages and phone calls.
Authorities became aware of the allegations last month after the victim told her friends about the relationship, and the friends went to the school principal with their concerns.
Prosecutors also said Mejia tricked other employees into helping him cover up the assaults, but they didn't know about the alleged abuse.
"We don't believe they were aware what was going on. One employee that was told to cover up the cameras with tape was told that they were going to be painting them," said Deputy District Attorney Robert Mestman.
Mejia is on administrative leave and free on $250,000 bail. The judge ordered Mejia to stay away from all schools.
"There's no reason for him to be on a school campus, so we thought, for the safety of the public, that was appropriate," Mestman said.
Parent Rosa Martinez said the incident makes her worried for her own child.
"You try to protect your children, and you think they're safe at school," she said.
If convicted on all counts, Mejia faces up to nearly 13 years in prison. He will be back in court in July for a preliminary hearing.
Relatives did not comment to Eyewitness News after the arraignment.
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