Most doctors – and the American Academy of Pediatrics (AAP) — agree that a normal body temperature for a healthy baby is between 97 and 100.3 degrees Fahrenheit.If your baby's rectal temperature is 100.4 degrees or higher, he has a fever.ost doctors – and the American Academy of Pediatrics (AAP) — agree that a normal body temperature for a healthy baby is between 97 and 100.3 degrees Fahrenheit.