Aaron John McLeod stood trial in the NSW Supreme Court after pleading not guilty to murdering the toddler in May 2022 at his partner's home in Coffs Harbour, on the NSW mid-north coast.
Neither the child nor his mother can be identified for legal reasons.
The 40-year-old was accused of going into the boy's room and inflicting injuries, including fracturing his pelvis and ribs, while the boy's mother was asleep in the house.
On Monday, a jury found McLeod guilty of murder after three days of deliberations.
He was convicted and taken into custody, with Justice Phillip Boulten noting he was facing "the inevitability" of a full-time jail sentence.
McLeod had expressed his frustration with the toddler's behaviour multiple times despite only knowing his mother for two months, the jury was told.
He had called the two-year-old an "out-of-control c*** who needs to be sorted out", crown prosecutor Ben Allison said during his opening address.
The boy's mother became emotional as she gave evidence about McLeod grabbing the child and holding him during toilet training.
"(McLeod) was quite annoyed ... he believed that (the boy) was quite naughty," she told the jurors during the trial.
The boy had fallen down a set of slippery steps and banged his head on the afternoon before he died, the court was told.
He was also found banging his head on the floor in the middle of the night hours before he died.
But the Crown said the incidents did not explain his fatal injuries.
The boy's mother testified that he seemed fine and showed no signs of injury after the accidents.
McLeod's barrister David Price had argued there was no evidence linking his client to any physical abuse of the toddler either on the night he died or in the two months beforehand.
The child's blood on McLeod's t-shirt was the result of his attempts to resuscitate the boy, Mr Price told the jury.
The two-year-old died after suffering catastrophic injuries including a brain haemorrhage and a fractured pubic bone.
McLeod will be sentenced in October.
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