Admission into JSS 1 and transfer of students into Nigerian Navy Secondary School is the sole prerogative of the Naval Headquarters through the Directorate of Naval Education.

Fresh admission into NNSS is conducted through a centrally coordinated entrance examination usually organized by the Naval Headquarters through the Directorate of Naval Education. Successful candidates in the final interview are issued admission letters and acceptance forms from the Naval Headquarters through the Directorate of Naval Education.