A group of female family members along with a baby were in court supporting the woman.
The woman's 29-year-old boyfriend, who was in jail, was also charged on Wednesday with murdering the child.
Earlier this year the man was charged with 25 offences including assault, child neglect, taking action resulting in injury or sex abuse and producing child abuse material.
The little boy was found dead in the early hours of May 21 in a unit in Oatley, in Sydney's south.
Family members had called paramedics, telling them the child had sustained head injuries after falling from a pogo stick the previous day.
Detectives will allege the injuries were not accidental.
A court has already heard the boy suffered "deplorable, prolonged abuse".
He was allegedly reduced to begging for water from shocked campers in the Illawarra two months before he was found dead, the court was told at the man's September bail hearing.
A police statement of facts previously tendered in court said an autopsy showed three fractured ribs, a bruise in the shape of a fist, feet injuries and bruises to the boy's legs, back and buttocks that were inconsistent with normal childhood injury.
The boy and his two younger siblings had been previously well cared for, but police allege that changed dramatically after the family moved early this year to the man's studio, which was windowless and had no toilet.
NSW State Crime Command Homicide Squad Commander Mick Willing on Wednesday described the case as among the most horrific he has ever seen.
"The circumstances surrounding the death of this child involve some of the most distressing acts that we've ever seen," he told reporters.
-AAP
