Being located alongside the Navy workshops and stores, the club house played an important role during World War II. The RAN took over the downstairs area of the club house in 1941 as headquarters of the Naval Auxiliary Patrol, while the upstairs area continued to be used for dances and fund-raising events for the Australian Comforts Fund. Club members who were either too young or too old to enlist in the forces, provided valuable service with the Naval Auxiliary Patrol in assisting the operation of Cairns’ harbour boom defence system and in harbour protection generally.

The club rooms remained a popular local venue for social functions in Cairns until the 1980s when high-rise hotel development began to take place alongside the building. However, the Cairns Yacht Club still retains its membership and its important function of training young competition sailors.