No. 458 Squadron was formed at Williamtown, New South Wales, on 8 July 1941 as an Article XV squadron under the terms of the Empire Air Training Scheme. Consisting of only ground staff, the squadron departed for the United Kingdom in August to join other personnel assembled at RAF Holme-on-Spalding Moor, where the squadron was officially established as No. 458 (Bomber) Squadron on 25 August 1941. From the outset, the squadron drew personnel from many different countries, with many coming from Britain, Canada and New Zealand, as well as Australia.

Equipped with Wellington Mk.IV bombers, No. 458 Squadron formed part of No. 1 Group RAF of Bomber Command. It participated in its first operational sortie on 20/21 October, when ten of its aircraft joined in night attacks made against the ports of Emden, Antwerp and Rotterdam. Further attacks were made against industrial targets in France and Germany over the course of several months as part of a strategic bombing campaign. In addition, the Wellingtons were involved in mine-laying operations along enemy occupied coasts. In late 1941, No. 458 Squadron provided a flight to help raise the newly formed No. 460 Squadron RAAF. At the end of January 1942 the squadron was withdrawn from Bomber Command to serve in the Middle East.

A Wellington Mark X illustrating the geodesic construction and the level of punishment it could absorb while maintaining integrity and airworthiness.

For its service during the war, the squadron was awarded six battle honours: Fortress Europe 1940–1944, France and Germany 1944–1945, South-East Europe 1942–1945, Mediterranean 1940–1943, Sicily 1943, and Italy 1943–1945.