Nathan Gastineau, 30, was arrested in April. He is a 10-year veteran of the department, and he faces a number of felony charges, including three counts of a lewd act on a minor and three counts of unlawful sex with a minor.
He entered a not guilty plea and was released on $150,000 bail.
The alleged victim was also in court.
"She wanted to come to court today. She wants to stand here and let people know that she will not be intimidated, and that she will demonstrate courage in this case, and that's what she's doing," said Attorney Gloria Allred, who is representing the victim.
Allred said she is going to protect the rights of the victim and the criminal case works its way through the courts.
Gastineau was in charge of the Explorer program at the Highland Station where he was assigned. According to the victim's father, Gastineau met the victim through the program.
She was one of the Explorer scouts who was on a ride along with him at the time of the alleged crimes. Officials say Gastineau and the teenager had an ongoing relationship.
The ride-along portion of the Explorer program in the San Bernardino County Sheriff's Department was suspended for 60 days after more accusations about unlawful sex with a minor came to light - this time involving another deputy in Victorville. Deputy Anthony Benjamin is facing two similar charges. He is currently on paid administrative leave.
Gastineau is no longer with the sheriff's department, but family members of the alleged victim are still concerned that what might have happened by someone who carried a badge and was trusted by the public.
After Gastineau's initial arrest, the alleged victim's father called the former deputy a predator.
"He's worse than other predators because he has a badge," he said.
After the arraignment, neither Gastineau nor his attorney would comment on the charges. Gastineau is scheduled to appear in court again on Aug. 2.