Police say 46-year-old Jeffrey Mackintosh was arrested Thursday night at his Phillipsburg home.
He faces charges of sexual assault and endangering the welfare of a child.
Mackintosh is in custody on $150,000 bail and it's not clear if he has a lawyer.
Prosecutors say the child victim, who is now an adult, contacted the Perth Amboy authorities on July 5 to report the abuse.
Investigators say that Mackintosh, now a computer technician, had allegedly repeatedly sexually assaulted the boy in the year 2000, while serving as youth pastor at the Glad Tidings Assembly of God Church.
He is no longer affiliated.
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