Lisa Rose Halcrow, 40, appeared in Warwick Magistrates Court on Tuesday morning following her arrest on Monday.
Connor, 2, died at Warwick Hospital after suffering multiple head injuries in August 2018, police say.
He was in the care of Ms Halcrow at the time of his death and police were initially told Connor had fallen down the stairs.
Ms Halcrow has been charged with one count of murder and one count of grievous bodily harm following an 18-month investigation by police.
The case was adjourned until May 6. She has been remanded in custody.
Connor’s death was brought back into the public eye when his family made a plea for anyone with information to come forward.
Two Warwick homes and a car were then turned into crime scenes.
“This was a very tragic incident and our detectives have been committed to finding answers for Connor’s family,” Detective Acting Inspector Matt Howard said on Monday following the arrest.
“I’d like to particularly thank the members of the public who assisted the investigative team over recent weeks with valuable information to the case.
“I think there will be a bit of relief for the members of the community in Warwick.”