The principal at the Caledonia-Mumford Middle School has agreed to resign.
Paul Estabrooks had been reassigned to the district office before the start of the school year.
The Livingston County News had reported that at least three teachers had accused Estabrooks of harassment, sexual harassment, gender discrimination, and retaliation over five years.
The state Division of Human Rights found probable cause for allegations of discrimination brought in a lawsuit in 2017.
Under a separation agreement approved by the school board, Estabrooks will be paid until next October.
The board says the agreement avoids a potentially lengthy and costly hearing process.