The Garner Police Department said the boy died of internal injuries and 22-year-old Deysi Yhuriko Martinez is accused of not getting him medical treatment in a timely manner.
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Police said it happened in August at an extended stay hotel on Hwy 70 in Garner.
At a first court appearance on Thursday, a prosecutor said the child died just days short of his 4th birthday after suffering an intestinal tear.
"Wake Medical Center was unable to successfully repair the tear to his intestines. It had caused sepsis and the infection is what killed him," said Wake County Assistant District Attorney Melanie Shakita. "The state's position is that had she sought medical care for her child that he likely would not have died."
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"It had to be obvious that this child had some kind of internal injuries and the parents should have known. The mother should have known that that child needed emergency care and she didn't provide that in a timely manner," Capt. Joe Binns with the Garner Police Department told ABC11.
Detectives are still working to learn how the boy was injured.
"What caused this injury? When did this injury actually occur? How did that injury occur? So there's just a lot of pieces that we don't have yet," said Capt. Binns.
Shakita shed more light on the investigation at the court hearing.
"The investigation is ongoing into her boyfriend who was alone with the child at the time," she said.
Shakita also said Martinez has five previous arrests in Wake County and has a history of not showing up for court appearances. Based on that, the judge raised her bond from $150,000 to $500,000.