Its construction, without benefit of new equipment or funds apportioned by the United States Congress due to agreements reached during the Washington Naval Conference,[4][5] began in 1932 and the main tunnel and 25 laterals were completed in 1934.

[6] The Army Corps of Engineers rented obsolete equipment from Baguio gold miners for a nominal fee and made do with condemned TNT from the Ordnance Department.

At the vicinity of the tunnel's west entrance in the afternoon of 30 December 1941, Manuel L. Quezon and Sergio Osmeña took their oaths of office as President and Vice-president of the Philippine Commonwealth in simple ceremonies attended by members of the garrison.

Today, Malinta Tunnel is the venue of an audio-visual presentation by National Artist Lamberto V. Avellana of events that occurred during World War II, including the evacuation of President Quezon and General MacArthur by Motor Torpedo Boat Squadron Three from Corregidor to Mindanao.

Further concurring to its haunted reputation is collapsed sections of the tunnel, brought about by detonation from Japanese soldiers who committed suicide during World War II.