Ihaka Paora Braxton Stokes, who was 15 months old, died in hospital after being found unconscious at a property in Bryndwr on 3 July.
The accused also faces a second charge of assaulting the toddler the day before he was found unconscious.
The man has been granted interim name suppression to give him time to inform his parents of his arrest.
His lawyer, Philip Shamy, asked for his client to be released on bail, which police opposed.
Judge David Saunders said given the serious nature of the charges, arguments would need to be heard from both sides before a decision could be made on bail.
He instructed the lawyer to apply for a bail hearing in front of another judge later today.
The accused man is due to appear in the High Court on 31 July.