Nairana Study Centre is run by a Director and leadership team. The current Director is Mr Richard Vella. The team is composed of residential staff and several volunteers, including senior high school and university students.

The residential chaplain, a Catholic priest of the prelature of Opus Dei, is available for personal spiritual direction and administration of the Catholic sacraments. The leadership team is supported by parents in the form of a Develop Committee and Parents Committee (DEVCO). The continued success of Nairana depends on the generous dedication and input of many parents.