According to Alief ISD police, the student said Allison told him, "I'm tired of you." The student said Allison punched him and pushed him to the floor, sitting on him.
Administrators told Allison to get off the student, and he was taken to the office, police said.
KIAH reported that Allison admitted to holding the boy on the floor, but did not recall hitting him.
"The Harris County District Attorney's Office has charged Alief employee Lisa Allison with injury to a child following an investigation by Alief ISD Police and district administrators," the district said in a statement to The Houston Chronicle.
"Allison was immediately placed on leave when allegations were brought to the attention of campus and district administrators, and will not return."