Holly Back, 40, and Mousa Hawa, 41, of Chester County are charged with third-degree murder, involuntary manslaughter, and other related charges.
Medics were called to their home on Lincoln Highway East in Coatesville on July 26 for reports of a child in cardiac arrest.
At the scene, investigators say they found a home filled with drug paraphernalia.
"There was a box of literally hundreds of used heroin baggies that had been kept," said Chester County District Attorney Chris de Barrena-Sarobe. "What's worse, with all the drug use signs around, they completely denied being drug users on the scene, which doesn't help medical responders treat a child."
According to investigators, the child had fentanyl, cocaine, and other drugs in his system.
Investigators said the parents deliberately left deadly drugs out in the open.
In the affidavit obtained by Action News, Hawa said his son knew not to touch the drugs, calling them "daddy's medicine."
The charges come nearly a year after Hunter died. Investigators said it took time to gather all the evidence, including toxicology results, and discuss the case with experts.
In the time since their son's death, Hawa and Back started a GoFundMe page soliciting donations in their son's name.
The page stated that their son "passed suddenly" and "we loved him with all our hearts." It has raised roughly $895 with a goal of $2,500.
"This is just clearly not the case where I think these parents deserve a dollar from anybody, considering what they did to the child," said de Barrena-Sarobe.
According to the affidavit, throughout Hunter's short life, there were red flags. Doctors reportedly expressed concern about his poor vision and language delay.
He was also in and out of the hospital for injuries that staff suspected were signs of abuse.
Hair samples also show that the child had been exposed to drugs in the past.
Back is being held in jail on a $1 million bond. Hawa was already housed in the Chester County prison on other drug charges.