Stein's bond was originally set at $200,000, but was lowered to $100,000 during her first appearance in court Friday.
She has relinquished her passport, and has promised not to have any physical contact with her children pending resolution of the charges.
In mid-March, police say Stein and her husband called 911 to report that Adam Stein, 3, who was adopted from China, and who neighbors say has learning disabilities, had fallen down a flight of stairs.
Last week, Apex police served a search warrant on the couple's home - seizing family photos and a phone bill.
Following the search, Eyewitness News spoke to about half a dozen neighbors, all of whom were shocked at the investigation, and were certain the Steins name would be cleared.
In an affidavit, the detective investigating the case describes a history of abuse and neglect reports related to the child. He also says the Steins have been uncooperative - refusing to speak to investigators.
Philip Stein, the boy's father, has not been charged in the case. The couple also has a daughter, who is never mentioned in any of the abuse allegations.
The Steins' family lawyer told ABC 11 on Friday that he looks forward to learning what sort of evidence the State will present in the case.
Apex Police Chief Jack Lewis says there's a reason Stein faces a charge of felony child abuse.
"The charge is based upon the conflict between the medical opinion on the nature of the injuries and how that could have occurred as compared to the version that was presented by the mother," he explained.
According to search warrants there have been two other incidents of neglect or abuse.
One involved bruises observed by a daycare worker. More serious was what happened in the home in January. The boy suffered 2nd and 3rd degree burns on his hands during a bath.
Child Protective Services called it a case of bad parenting and told police they didn't need to investigate.
"If police had gotten the information first instead of Child Protective Services we may have very easily reached exactly the same conclusion as they did," said Lewis
Police aren't questioning Child Protective Services, but they would like to talk to the little boy who is still fighting for his life.