The accused, surnamed Liu, raped the student in March 2012. He had not been arrested until last week.
The local publicity office declined to explain why it took more than a year to make the arrest.
The age of the victim was not disclosed, state-run Xinhua news agency reported.
Liu, now in his 50s, served as headmaster of a school in Ningshan County for 10 years. He was transferred to the county's education bureau in 2012.
A string of school rape and molestation scandals sparked a public outcry earlier this year.