Police say Steven Fulton, 26, from the 5000 Block of Osage Avenue, repeatedly assaulted the girl over a three-year period while he a teacher at Timothy Academy, a Christian school in North Philadelphia.
Capt. John Darby says some of the alleged assaults took place at the school and escalated as time went on.
Other incidents took place inside Fulton's vehicle and other locations in the city, Darby said.
Police were contacted after the now-14-year-old girl told another adult at the school she'd been assaulted.
Fulton was arraigned Wednesday on charges including rape and sexual assault and released on bail.
In a statement, the Timothy Academy said it has fired Fulton.
At the school on Wednesday afternoon, parents said Fulton was popular with the kids. His religious faith was even captured on a music video he uploaded to YouTube. Some were dumbfounded by the news.
"I'm not going to be the spokesperson for everybody, I'm just a parent that's in shock right now," one father said.
However, at least one parent didn't believe the allegations against Fulton.
"Whatever they said he did, he didn't do," said another father. "It's just a little kid looking for attention."
Parents of some of the students at the school said Fulton was the victim's coach.
Darby recommended parents of Timothy Academy students calmly talk to their children about this situation and, if they had any questions, to contact the Special Victims Unit of the Philadelphia Police Department.