Police arrested the 40-year-old woman in Warwick on Monday following an 18-month investigation.
Police were told Connor, who was in the care of his babysitter, had fallen down stairs.
He died in hospital on August 19, 2018 from multiple injuries.
Connor’s family made a public appeal in January for anyone with information to come forward.
Days later police searched two Warwick houses and one vehicle as part of their investigation into the boy’s death.
The babysitter was also charged with one count of grievous bodily harm.
“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.
“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.”
The babysitter will appear in the Warwick Magistrates Court on Tuesday.