Police said the "poop smell" disrupted classes, triggered health issues, and cost the school district nearly $55,000 in damages.
Devon Murphy, who also served as the boys' varsity basketball coach, was charged with assault by strangulation and misdemeanor child abuse.
The teacher has worked at Howard Learning Academy and Douglas Byrd High School.
The incident occurred at Smith Magnet Elementary School, deputies say.
An instructional assistant in special programs at Lead Mine Elementary School in Raleigh was arrested for allegedly assaulting another woman.