School resource deputies requested a welfare check on Friday for the boy, Ra'myl Pierre, after he had been missing from school for two weeks.
A deputy went to the home that morning and met the boy's mother, 31-year-old Rhonda Paulynice, who led the deputy into the bedroom where he found the boy dead in his bed.
St. Lucie County Sheriff Richard Del Toro said the child's cause of death was not immediately apparent and that an autopsy was scheduled for Saturday.
While interviewing Paulynice, detectives learned that she had last spoken to the child on May 18, which is when they believe the homicide occurred, the sheriff said. He had been missing from school since May 14.
Deputies had been at the home for a medical issue the mother was having just a day before they believe the boy was killed, on May 17.
"What we did learn in speaking with the mother is she believes she was being told by God to basically exorcise demons out of the child's body," Sheriff Del Toro said.
She has been charged with second-degree murder, failure to report a death and altering a body.
Del Toro said that the mother told investigators that when the child stopped moving, she believed he had been freed of the demons, and she was waiting for him to "come back."
No one else was living in the home at the time.
"From what I understand, this kid just lit the room up and was loved by everybody," the sheriff said.