Karen N. Hooks, 33, of Squire Circle in Dover, has been charged with abusing a corpse after the body was found on Wednesday.
However, she has not been charged in connection with the death at this time.
Delaware State Police say the investigation began as a missing child complaint back on July 9th.
Detectives said the tipster was concerned because Hooks, the mother of a 2-year-old, had been due to give birth in June to another baby, but that baby was nowhere to be found.
Police say they contacted Hooks on July 13th who told them her two-year-old son, Justice, was in the care of a female friend. She also allegedly denied ever being pregnant.
Detectives say they were unable to verify the story of Justice's whereabouts and obtained a search warrant for the home on Squire Circle, which was served on Wednesday.
Police say, during the search, they found a "suspiciously wrapped package" in a storage area shared by Hooks and a roommate.
The contents were taken to the Medical Examiner's Office and were determined to be that of a boy who was at least one year old.
The ME said the manner of death is "homicide by blunt force trauma to the head."
Police say the body is presumed to be that of Justice Hooks. However, official confirmation is still pending.
Police also say they have not been able to confirm that Hooks was ever pregnant.
Hooks was arrested and was ordered to be held on $1,000 cash bail.
Homicide Detectives and the Medical Examiner's Office are continuing their investigation into the circumstances surrounding the death of the child and additional charges are possible.