Bail was set Tuesday at $250,000 cash for 44-year-old Michelle Heale of Toms River.
Heale was watching the child in her home on Aug. 28 when he started having breathing problems. The toddler was flown later that day to a children's hospital in Philadelphia, where he died three days later.
Doctors later determined that the boy suffered severe brain, spine and retinal damage from a violent shaking.
Heale's lawyer, Karl Mohel, says his client maintains her innocence.
The case will be heard in Monmouth County, because both the infant's father and Heale's husband both work for the Ocean County Prosecutor's Office.