Kevin Park is accused of killing Madison Horn at a property in Kelty, Fife, on April 20.
The 26-year-old made his first public appearance in the dock at the High Court in Glasgow.
The charge alleges Park shouted at Madison, pulled her hair, lifted the child up and repeatedly struck her head against a wall. It goes on to allege he bit the toddler on the body before repeatedly striking her again "by means to the prosecutor unknown".
Park pleaded not guilty plea and trial was set for November.