Timothy and Sarah Johnson face charges of neglecting their seven year old son in March 2015 when he became ill with pancreatitis and acute sepsis.
Prosecutors claim the boy would not have died if the couple, both committed Christians, had called for help instead of praying over his body.
Seth Johnson, who was adopted by the pair, was found collapsed on the floor when the parents returned from a weekend away.
Instead of immediately calling for help they prayed over his unconscious body, prosecutors claim.
Both of the parents allegedly have "issues going to doctors" and they were concerned about their son being put on medication.
When paramedics were eventually phoned they pronounced the child dead at the scene.
Hennepin County Attorney, Mike Freeman, said: "The parents admitted to police that his behaviour had changed, that he wasn't sleeping, was throwing himself down stairs and was taking hours to eat.
"Yet, they refused to do what most parents would have done and take him to a doctor."
He added: "The Johnsons, of course, are presumed innocent. But we are going to use all of our resources to prove them guilty of neglect of a child resulting in substantial physical harm and ask for the strongest penalty allowed under the statute and sentencing guidelines."
