9 Squadron RAAF was formed on 1 January 1939 when 5 Squadron RAAF was renumbered as 9 Squadron RAAF. 5 Squadron RAAF had been earlier formed at Richmond in New South Wales on 20 April 1936. The Squadron was equipped with Supermarine Seagull V amphibious aircraft. They were known as the Walrus by the RAF.

The Seagulls of 9 Squadron were attached to various RAN cruisers so were spread far and wide. The aircraft and its ground crew would be under the operational command of the ship's Captain. The Seagull was catapulted from the ship and would then later land near the ship and be picked up by a crane. The Squadron relocated to Rathmines in January 1940.

When WW2 broke out in Europe several Seagulls travelled to the Mediterranean on board their allocated cruiser. The remaining Seagulls operated in Australian waters. One Seagull captained by Flying Officer L.G. Webber, was attached to a New Zealand Cruiser HMNZS Achilles.

In December 1940, the Seagull attached to HMAS Canberra carried out a search for some German surface raiders reported to be off the West Australian coast. 

When Australia declared war with Japan in December 1941, a number of the cruisers with their Seagulls returned from the Mediterranean to operate in the South West Pacific Area (SWPA). 

Six members of 9 Squadron RAAF were killed when the German Raider Kormoran sank HMAS Sydney off the West Australian coast on 19 November 1941.

9 Squadron moved from Rathmines to the Bowen Flying Boat Base in north Queensland on 12 January 1943.

From 1943 the role of the cruiser-borne amphibious aircraft became less important due to the closer co-operation by the Royal Australian Navy with the US Navy and the increasing numbers of aircraft carriers in the SWPA.

9 Squadron personnel moved out of Bowen Flying Boat Base on 30 November 1944 by train headed south for Rathmines.

By late 1944 all RAN cruisers had relinquished their amphibious aircraft and removed their catapults. 9 Squadron was then disbanded at Rathmines on 31 December 1944.