West Australian police say the 25-year-old attacked the child in her bedroom about 12:30am on Monday after scaling a fence and breaking into an Ellenbrook family's home.
He was arrested on Wednesday after police released footage of a man climbing over a wall near the home in Perth's northeastern suburbs.
He was charged with sexual penetration of a child under 13, indecent dealings with a child under 13, deprivation of liberty and aggravated home burglary.
He is also facing two charges of impeding another person's normal breathing or blood circulation by blocking their nose or mouth and applying pressure to their neck.
The girl's parents learned about the assault later on Monday morning when the child told them she had been sexually assaulted during the night.
The CCTV footage shows a man wearing shorts and a T-shirt walking near a wooden fence before he climbs up and peers into a backyard.
He then walks away before returning a few minutes later with a backpack and jumping over the fence.
The girl's pyjama top, which had a gingerbread man wearing a Santa hat on it, was missing from the home.
The man will appear in the Midland Magistrates Court on Thursday.
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