Officers were called to a property in Croftangry Road in Kelty, Fife, at 6.30pm on Sunday.
Two-year-old Madison Horne was taken to Victoria Hospital in Kirkcaldy, where she was later pronounced dead.
Police Scotland said that a 26-year-old man has been charged with murder and will appear at Dunfermline Sheriff Court today.
Teddy bears, soft toys and pink roses have been left at the gate of the two-storey house in Kelty by passing residents.
A teddy was laid with the note: “Rest in peace little Madison, now you’re in the arms of the angels.”