Ronan Davies, aged 17 months, died last month after being rushed to hospital with what was described as severe head and internal injuries.
Quentin Corrigan, 30, is accused of inflicting injuries on the boy while babysitting him last month.
Corrigan allegedly returned Ronan with head and internal injuries from which he would not survive.
Corrigan was arrested by major crime detectives on Tuesday following an investigation at the Glenelg North unit complex, where he had been babysitting Ronan early last month.
It is alleged that shortly after returning the toddler to his Ottoway home, his father found him unconscious and rushed him to the Women's and Children's Hospital.
He died there two days later.
Ronan's parents were at court for Corrigan's first court hearing where he didn't apply for bail.
The case will return to court in April next year.
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