Video of the incident spread on social media and now new surveillance video appears to show the officer putting his knee on the girl's neck during a fight at Lincoln Middle School.
The student's father told ABC News she suffered injuries to her head and neck.
The officer worked for the district part time, officials said.
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In a statement, the school district said in part, "it is aware of an incident that happened between two students and the officer is currently on paid leave from the district."
Officials said an internal employment investigation will now conclude with his resignation.
The Kenosha Police Department said, as of Saturday, the officer is still employed with KPD.
"KPD is aware of [the officer's] resignation from the school district and the verbal notice of claim made by an attorney representing the student... We continue our investigation, paying careful attention to the entire scope of the incident. We have no further update at this time," the department said in a statement.