After commissioning HMS Indomitable sailed to the West Indies for work-up. Had it not been for her grounding in Jamaica while working up in November 1941, Indomitable might well have been sunk the following month, as she was originally intended to join the battleship HMS Prince of wales and the battlecruiser HMS Repulse at Singapore, both those ships were sunk in December 1941.

In January 1942, she joined the Eastern Fleet at Ceylon and ferried RAF Hurricanes to Java at the end of that month. She took part in Diego Suarez operation with HMS Illustrious in May 1942, and exercised with the RAF off Ceylon in June 1942. In May 1942, HMS Indomitable sailed to Madagascar to attempt to seize a French Navy base at Diego Suarez in order to prevent the Japanese from using it as a submarine base.

Indomitable took part in the operation "Pedestal" Malta convoy on 3 August 1942. Indomitable had her flight-deck armour pierced by an 1100lb bomb, in the Mediterranean in August 1942 when enemy bombers scored 2 hits and 3 near-misses; that and another hit aft where there was no armour put her out of action being repaired in the USA until February 1943. Indomitable sailed to the Mediterranean in February 1943, and was torpedoed on 16 July by an Italian S79 aircraft(pilot Caselli) while covering the Sicily landings. She underwent repairs in USA from July 1943-February 1944.

She then joined the Eastern in June 1944 for air strikes against targets on Sumatra with HMS Victorious on 29 August and 18 September, 1944. This was followed by air strikes against the Nicobar Islands with HMS Victorious on 17 and 19 October. She was involved in an unsuccessful attack on Medan, Sumatra, with HMS Illustrious on 20 December 1944. On 4 January 1945, she took part in a successful air strike against Medan, with HMS Indefatigable and HMS Victorious, and then immediately afterwards was involved in further strikes against refineries in Palembang, Sumatra on 24 and 29 January 1945.

Indomitable was in Sydney to join the British Pacific Fleet in February 1945, returning to active duties with air strikes against Sakishima Gunto and Formosa in March-April 1945. On 4 May she was hit by a Kamikaze - but received no damage -the Kamikaze aircraft simply slid up the armoured flight deck and over the side. She later arrived back at Sydney for a refit in June 1945. She again departed from Sydney in mid-August for the re-occupation of Hong Kong, her aircraft flying their last combat missions on 31 August and 1 September against Japanese suicide boats at Hong Kong.

She finally returned to the UK in November 1945 with British personnel from Australia having ditched all her aircraft overboard off Sydney Post war Indomitable was involved in two more repatriation voyages in 1946, she then was put in reserve and undertook a refit between 1947-50. She again was active in the Home Fleet between 1950-53, but reduced to reserve on the Clyde on 5 October 1953. She was sold for scrapping in October 1955.