Greene County prosecutors charged Craig Michael Wood, 45, with murder, child kidnapping and armed criminal action Wednesday.
The charges come hours after the body of 10-year-old Hailey Owens was found inside his home.
Owens disappeared while walking near her home on Tuesday.
Witnesses told police that Hailey was taken by a man in a pickup truck. The abduction prompted an Amber Alert.
Wood was a coach and teacher's aide in the Springfield School District. He has been suspended.
Police say the two apparently did not know each other.