Liam Whoriskey, of Glenabbey Gardens in Derry, denies murdering Kayden McLaughlin-McGuinness nearly two years ago.
Kayden was found dead in the child’s family home at Colmcille Court on September 17, 2017.
On Friday, a judge at Belfast Crown Court listed the trial of 25-year-old Mr Whoriskey to begin on 3 September at Derry Crown Court.
A jury is to be sworn in that day, with the case to be opened by the prosecution the following day.
No details surrounding the case were given during the short hearing, however, a previous Crown Court hearing heard that the case could involve complicated medical issues in relation to pathology, and in particular neuropathology.
A hearing in June last year heard a detective tell a judge that Kayden had sustained 13 blows to the head.
The officer described it as a “blunt force attack”.
The court heard Kayden would have survived for only 30 minutes after suffering the fatal blow.
A post mortem examination also revealed the toddler had sustained a rib fracture, between six and 10 days before his death.