Robert E. Lee Academy is governed by a Board of Directors elected by the parents. The Board of Directors is responsible for the financial well-being of the school, strategic planning and developing policy for the school administration to implement. The categorical purpose of the Board is to preserve the existence, values, mission and philosophy of Robert E. Lee Academy.

The Board of Directors does not involve itself in day-to-day operations of the school. The Head of School and administrative staff are in charge of the day-to-day operating decisions regarding the Academy. All grievances and appeals should be directed to the Head of School or other appropriate faculty/staff member.

Board meetings are held the fourth Monday night of each month with the exception of December. Parents, teachers and students wishing to meet with the Board must meet with the Head of School in an attempt to solve their grievance. If unresolved at this level, a letter stating the problem and request for a Board audience must be mailed to the Board Chairman 10 days prior to the next scheduled board meeting.