Five-month-old Jack McLaren, from Newbury in Berkshire, died in hospital on 4 June, two days after an alleged attack.
Daniel McLaren, of Fleetwood Close in Newbury, has been charged with murder. He appeared at Reading Crown Court via video link from prison earlier and entered a not guilty plea.
A trial has been scheduled to begin on 22 January 2018.
A 29-year-old man has denied murdering his baby son.