Jennifer Clark, who is 38, and 34-year-old Jeromie Clark are charged with criminal negligence causing death and failure to provide the necessities of life.
Their 14-month-old son, John, died in hospital in November 2013.
Police say he was brought to hospital the day before he died.
They say the child had an untreatable infection that was complicated by malnutrition.
Lawyers are to seek bail for the couple on Tuesday.
The Clarks appeared in court on closed-circuit television.