Fulton was charged with rape, predatory sex assault against a child, criminal sex act and acting in a manor injurious to a child.
Prosecutors say when the victim turned 12, Fulton touched her and exposed himself. Police say they had sexual intercourse for the first time when the victim was 12.
According to police, the investigation further revealed that Fulton's conduct came to light when the victim's mother learned that another young girl that attended the center complained of the defendant's behavior toward both girls.
Fulton, who lives on the Lower East Side, was arraigned in Manhattan Criminal Court.
The youth minister was accused of sexually abusing a girl who attends his Baptist church.
Prosecutors believe there are other victims. They are appealing for other children who were abused to contact them
Defense attorney Liz Beal says Fulton has worked at the church for seven years and is highly regarded. She says the church held a meeting after his arrest and that no other allegations surfaced.
Henrietta Carter, a pastor at the church, said she had no comment at this time.
The Mariners' Temple Baptist Church, founded in 1795, is the oldest Baptist church in Manhattan.