The superintendent is appointed by the school board. In 1993, Bertha Pendleton was selected as the superintendent. She was the first woman and first African American in the position and she served to 1998. From 2010 through 2013 the superintendent was Bill Kowba, a retired Navy rear admiral. On February 26, 2013, Kowba announced his retirement, effective June 30. The next day, February 27, the school board unanimously appointed elementary school principal
Cindy Marten as the new superintendent. The quick appointment, without a search process or community input, was described as "highly unusual - virtually unheard of" by
The San Diego Union Tribune. On May 18, 2021, Marten left her job as superintendent to become the
United States deputy secretary of education, with Lamont Jackson replacing her as the interim superintendent. Jackson was terminated in August 2024 after an internal investigation found that he had committed
sexual misconduct and retaliation against two former district management employees. Deputy Superintendent Fabiola Bagula took over as acting superintendent. == Partnership with Ocean Discovery Institute ==