Thirty-three-year-old Eric Clapper Sr. and 30-year-old Heather Almoney are charged in the Nov. 12 death of Eric Clapper Jr.
Authorities said in court documents that the baby was born premature. They allege that he died of dehydration and malnutrition.
Officials said Almoney told detectives that she tried to feed the child and give him vitamins and medicinal doses of caffeine daily.
Police told the York Daily Record that the boy weighed three and one-half pounds at the time of his death.
The defendants were taken to York County Prison without bail; a listed number for them could not be found and it was unclear whether they had attorneys.