Roy Kenneth Miller Jr is accused of causing substantial brain trauma to the victim by shaking him.
Officials say Carter Eugene Lizar died from those injuries on his first birthday.
Mr Miller told a judge during the video hearing he would apply for a public defender. A counsel-status hearing is scheduled September 11, ahead of the preliminary hearing September 25.
Mr Miller remains behind bars, unable to post $100,000 bail.
Abuse of a child resulting in death is a class-A felony, which carries upon conviction a prison sentence of not less than ten years and not to exceed thirty years, or life imprisonment.
The child’s mother, Sasha Lizar is charged with child endangerment. Police say she left young Carter for several days in a dangerous environment where methamphetamine was being used and in the custody of subjects who had used meth. Court documents also accuse Ms Lizar of using the drug while caring for the child.
A funeral is planned Wednesday at 5pm at the Rupp Funeral Home in St Joseph.