Leicestershire county council's solicitor is to convene an appeal panel next month to hear Liam Morris's complaint.
Mr Morris, 51, said one of the assault allegations stemmed from his legitimate restraint of a violent pupil; the other allegation was entirely fictitious. Both appear on his full Criminal Records Bureau disclosure when he applies for jobs.
The disclosure notes that in the first case, the Crown Prosecution Service decided not to prosecute due to conflict of evidence. In the second case, no formal complaint was ever lodged.
The National Union of Teachers said Mr Morris's problem was symptomatic of a wider malaise in which teachers' professional reputations were tarnished by malicious accusations.
Pauline Town, the union's divisional secretary, said Mr Morris was doing a tough job in a pupil referral unit, working with difficult pupils.
"Students can make false allegations against a teacher and management will jump into the child protection process and involve the police," she said. "It goes on your record, and it is a slur on your reputation that you can never remove."
Elizabeth McCalla, the county solicitor, wrote that Mr Morris's complaint raised "important issues of principle" about the council's role in involving the police.
Mr Morris's employer, the 70-pupil Blaby Pupil Referral Unit in Leicester, referred the two allegations against him last year to the county council, which called in the police.
He was suspended from March to October last year and then placed on paid leave until July this year. In the interim he applied for three jobs but was unsuccessful. He believes this was because of the assault allegations.
On the recommendation of Sir Michael Bichard following the inquiry into the Soham murders, schools must request enhanced Criminal Records Bureau checks on any prospective employee.
The enhanced checks include not just records of convictions, cautions, reprimands and police warnings, but also "other relevant information" that a chief police officer may choose.
Mr Morris said he was now denied opportunities to progress in his career or apply for jobs elsewhere.
"As teachers, we do understand and empathise with child protection. I've got two teenagers of my own," he said. "But the system seems to victimise teachers."
His partner, Stephanie Collyer, said is was difficult watching someone she cared about being "systematically destroyed".
"Liam's one of the most resilient people I know, but it's getting to the point where I see him potentially going under," she said.
John Dunford, general secretary of the Association of School and College Leaders, said headteachers did not want to deny a job to someone who had been falsely accused, but needed full information.
The Home Office said teachers could challenge information on their disclosures but it was up to police to decide whether it should be removed.
Leicestershire police said they had thoroughly reviewed Mr Morris's case. In a letter to him, they said the information about the allegations was accurate and factual and so should be made available to potential employers.