Lakeshia Baker and her boyfriend, Michael Scott, are charged with first-degree murder.
Prosecutors say, after killing the child, Baker claimed her son, Bryeon Hunter, had been kidnapped.
The boy's body has not been found.
Baker and Scott were in court Wednesday for a preliminary hearing.
Bryeon was reported missing last week. Baker initially told police three men attacked her and took off with the boy, prompting an Amber Alert. But prosecutors say Baker and Scott beat the boy when he wouldn't stop crying and dumped his body.