Michael Turnbull, 44, was suspended on full pay from Knowles Hill secondary in Newton Abbot, Devon, where he taught for 16 years, after the 13-year-old's parents claimed he hit her on the head with a textbook.
The school's inquiry - suspended when police launched their own investigation - has been re-opened now that he has been cleared of criminal charges.
Roger Darke, south-west regional secretary of the National Association of Schoolmasters Union of Women Teachers, said: "I am always concerned about these situations because someone who is not found guilty in a criminal court can still be guilty to the extent required for dismissal from their job."
Headteacher Colin Pope said: "The school disciplinary procedure was suspended when it became a police matter and now we must follow due process. The parents have been interviewed by my deputy. I have written to Mr Turnbull inviting him to come in and see me for an interview."
In throwing out the case, stipendiary magistrate Bruce Morgan said even if the book had made contact it was not deliberate.
After the case, Mr Turnbull said: "This fiasco has left me emotionally traumatised, socially stigmatised and professionally demoralised."
He has been advised to make no further comment until the
disciplinary hearing has been completed.