The first two counts were from the time the girl was in therapy with Avila. The third instance allegedly happened when the unidentified victim was no longer at Orangewood. Avila was accused of picking up the victim from her foster home and assaulting her outside.
A spokeswoman for the Orange County Social Services Agency said Avila was hired as a group counselor around 2006 after undergoing a background check, and that he met the minimum qualifications for the position.
A former resident of the shelter tipped off police in May 2008. Avila was arrested that month and charges were filed in 2010.
Avila, who is out of custody, will next appear in court in Oct. 8. He faces a maximum of four years and four months in prison, prosecutors said.
City News Service Contributed to this report