Terry Dusseault, 38, was wanted after disappearing with his 8-year-old son, also named Terry, from their home in Lumberton in Burlington County.
Police said the pair was found in Medford, New Jersey. The boy was not harmed.
The father is a registered sex offender.
The child's mother is deceased.
The Burlington County Prosecutor's Office said Dusseault was charged Tuesday with multiple counts of sexual assault against three juvenile victims. His son was not a victim in those charges.
Authorities went to arrest him at 301 Canal Circle, where he lives with his son and brother. His wife is dead. He knew investigators were looking for him so he took off with his son, officials said.