Sean Michael Mullender, 22, from Connah's Quay, was charged on Wednesday following baby Daniel's death in October 2014.
At Mold Crown Court on Thursday, Mr Justice Wyn Williams bailed him on the condition he stays at an address in Northumbria.
Mr Mullender's trial date has been set for next April.
North Wales Police were contacted by health officials after Daniel was admitted to the Countess of Chester Hospital on 2 October.
He was later transferred to Alder Hey Children's Hospital in Liverpool where he died on Saturday 4 October.
A Flintshire man who appeared in court charged with murdering his two-month-old son has been bailed.