Katie was found with serious injuries to her neck and upper body on a playing field in Woodthorpe, York, on 9 January and died later in hospital.
The 15-year-old, who cannot be named, appeared before Leeds Crown Court via video-link as her solicitor confirmed the not guilty plea.
She also denies a second charge of possession of an offensive weapon, namely a knife.
The girl did not speak during the 20-minute hearing but nodded as Judge Peter Collier QC asked if she understood the court proceedings.
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Family members were in court as Judge Collier, the recorder of Leeds, announced the trial would take place on 3 July.
She will remain in "local authority accommodation" until the trial, he said.
Katie's funeral was held earlier this week at York Minster, led by the Archbishop of York Dr John Sentamu.
An inquest into her death has been opened and adjourned.
A teenage girl has denied the murder of seven-year-old Katie Rough.