Burrell was still based at the Navy Office when World War II broke out in September 1939.
A reorganisation of the headquarters in May 1940 saw him promoted to commander and given the new role of Director of Operations, overseeing troop convoys and their air cover, local defence, and staffing issues.
Burrell's "full knowledge of Australian naval plans and resources" led to Prime Minister Robert Menzies personally nominating him to participate in staff talks with representatives of the Royal Navy and US Navy in October.
Soon after, he was posted as the first Australian naval attaché to Washington, D.C., in an effort to improve communications with the US in light of the threat from Japan.
Burrell was credited with helping to foster closer cooperation between the two navies in the Pacific region.
He also warned the Australian government that Britain and the US would adopt a "Germany-first" strategy in the event of war with Japan, and that the US was prepared to weaken its Pacific fleet to help secure the Atlantic.

Posted to Britain, Burrell was appointed commanding officer of the newly commissioned N-class destroyer HMAS Norman on 15 September 1941.
The ship's first operation was transporting a Trade Union Congress delegation led by Sir Walter Citrine to Archangel, Russia.
After returning to Britain, she steamed to the Indian Ocean to join Admiral Sir James Somerville's Eastern Fleet at Addu Atoll, Maldives, on 26 February 1942.
Following the Eastern Fleet's withdrawal to Kilindini, Kenya, Norman took part in the capture of Diego Suarez on Madagascar on 7 May. Later that month, she was reassigned to the Mediterranean and in June was involved in Operation Vigorous, an unsuccessful attempt to resupply the besieged island of Malta.
Transferred back to the Indian Ocean, Burrell led Norman in the second campaign of the Battle of Madagascar in September, and was mentioned in despatches on 19 February 1943 for his "bravery and resource" during the operation.
By this time Norman was escorting convoys in the Pacific, before deploying to the South Atlantic for anti-submarine duties in April–May.

On 23 June 1943, Burrell relinquished command of Norman and returned to the Navy Office, Melbourne, as Director of Plans.
Having been divorced from his first wife Margaret in November 1941, he married mineralogist Ada Weller (also known as Ada Coggan) on 21 April 1944; the couple had a son and two daughters.
Burrell took charge of the RAN's latest Tribal-class destroyer, HMAS Bataan, at her commissioning in Sydney on 25 May 1945.
Arriving on the scene too late to see action, the ship was deployed to Japan via the Philippines in July, docking in Tokyo on 31 August.
There she participated in the formal surrender ceremonies that took place on 2 September aboard USS Missouri.
Bataan remained in Japan as Australian Squadron representative until November, assisting with the repatriation of inmates from Japanese prisoner-of-war camps.
On a mission to one such camp at Sendai, Burrell located crewmen from the light cruiser HMAS Perth, which had been sunk in the early hours of 1 March 1942 during the Battle of Sunda Strait; 320 of her complement of 680 survived the sinking, 105 dying in captivity.
Burrell was still based at the Navy Office when World War II broke out in September 1939. A reorganisation of the headquarters in May 1940 saw him promoted to commander and given the new role of Director of Operations, overseeing troop convoys and their air cover, local defence, and staffing issues. Burrell's "full knowledge of Australian naval plans and resources" led to Prime Minister Robert Menzies personally nominating him to participate in staff talks with representatives of the Royal Navy and US Navy in October. Soon after, he was posted as the first Australian naval attaché to Washington, D.C., in an effort to improve communications with the US in light of the threat from Japan. Burrell was credited with helping to foster closer cooperation between the two navies in the Pacific region. He also warned the Australian government that Britain and the US would adopt a "Germany-first" strategy in the event of war with Japan, and that the US was prepared to weaken its Pacific fleet to help secure the Atlantic.
Posted to Britain, Burrell was appointed commanding officer of the newly commissioned N-class destroyer HMAS Norman on 15 September 1941. The ship's first operation was transporting a Trade Union Congress delegation led by Sir Walter Citrine to Archangel, Russia. After returning to Britain, she steamed to the Indian Ocean to join Admiral Sir James Somerville's Eastern Fleet at Addu Atoll, Maldives, on 26 February 1942. Following the Eastern Fleet's withdrawal to Kilindini, Kenya, Norman took part in the capture of Diego Suarez on Madagascar on 7 May. Later that month, she was reassigned to the Mediterranean and in June was involved in Operation Vigorous, an unsuccessful attempt to resupply the besieged island of Malta. Transferred back to the Indian Ocean, Burrell led Norman in the second campaign of the Battle of Madagascar in September, and was mentioned in despatches on 19 February 1943 for his "bravery and resource" during the operation. By this time Norman was escorting convoys in the Pacific, before deploying to the South Atlantic for anti-submarine duties in April–May.
On 23 June 1943, Burrell relinquished command of Norman and returned to the Navy Office, Melbourne, as Director of Plans. Having been divorced from his first wife Margaret in November 1941, he married mineralogist Ada Weller (also known as Ada Coggan) on 21 April 1944; the couple had a son and two daughters. Burrell took charge of the RAN's latest Tribal-class destroyer, HMAS Bataan, at her commissioning in Sydney on 25 May 1945. Arriving on the scene too late to see action, the ship was deployed to Japan via the Philippines in July, docking in Tokyo on 31 August. There she participated in the formal surrender ceremonies that took place on 2 September aboard USS Missouri. Bataan remained in Japan as Australian Squadron representative until November, assisting with the repatriation of inmates from Japanese prisoner-of-war camps. On a mission to one such camp at Sendai, Burrell located crewmen from the light cruiser HMAS Perth, which had been sunk in the early hours of 1 March 1942 during the Battle of Sunda Strait; 320 of her complement of 680 survived the sinking, 105 dying in captivity.
Henry Burrell (admiral)