During the Japanese occupation of the islands in World War II, there was an extensive Philippine resistance movement (Filipino: Kilusan ng Paglaban sa Pilipinas), which opposed the Japanese and their collaborators with active underground and guerrilla activity that increased over the years. Fighting the guerrillas – apart from the Japanese regular forces – were a Japanese-formed Bureau of Constabulary (later taking the name of the old Philippine Constabulary during the Second Republic), the Kenpeitai (the Japanese military police), and the Makapili (Filipinos fighting for the Japanese). Postwar studies estimate that around 260,000 people contributed to the anti-Japanese underground resistance in one way or another. Such was their effectiveness that by the end of World War II, Japan controlled only twelve of the forty-eight provinces.

Select units of the resistance would go on to be reorganized and equipped as units of the Philippine Army and Constabulary. The United States Government officially granted payments and benefits to various ethnicities who have fought with the Allies by the war's end. However, only the Filipinos were excluded from such benefits, and since then these veterans have made efforts in finally being acknowledged by the United States. Some 277 separate guerrilla units, with 260,715 individuals officially recognized as having participated in the resistance movement.

The attack on Pearl Harbor (called Hawaii Operation or Operation AI by the Japanese Imperial General Headquarters) was a surprise military strike conducted by the Imperial Japanese Navy against the United States naval base at Pearl Harbor, Hawaii, on the morning of December 7, 1941 (December 8 in Japan and the Philippines). The attack was intended as a preventive action in order to keep the U.S. Pacific Fleet from interfering with military actions Japan was planning in Southeast Asia against the overseas territories of the United States, the United Kingdom, and the Netherlands.

Immediately after the attack on Pearl Harbor, the Japanese operations to invade the Commonwealth of the Philippines began. Twenty-five twin engine planes bombed Tuguegarao and Baguio in the first preemptive strike in Luzon. The Japanese forces then quickly conducted a landing at Batan Island, and by December 17, General Masaharu Homma gave his estimate that the main component of the United States Air Force in the archipelago was destroyed. By January 2, Manila was under Japanese control and by January 9, Homma had cornered the remaining forces in Bataan. By April 9, the remaining of the combined American-Filipino force was forced to retire from Bataan to Corregidor. Meanwhile, Japanese invasions of Cebu (April 19) and Panay (April 20) were successful. By May 7, after the last of the Japanese attacks on Corregidor, General Jonathan M. Wainwright announced through a radio broadcast in Manila the surrender of the Philippines. Following Wainwright was General William F. Sharp, who surrendered Visayas and Mindanao on May 10.

Afterwards came the Bataan Death March, which was the forcible transfer, by the Imperial Japanese Army, of 60,000 Filipino and 15,000 American prisoners of war after the three-month Battle of Bataan in the Philippines during World War II. The death toll of the march is difficult to assess as thousands of captives were able to escape from their guards (although many were killed during their escapes), and it is not known how many died in the fighting that was taking place concurrently. All told, approximately 2,500–10,000 Filipino and 300–650 American prisoners of war died before they could reach Camp O'Donnell.

After Bataan and Corregidor, many who escaped the Japanese reorganized in the mountains as guerrillas still loyal to the U.S. Army Forces Far East (USAFFE). One example would be the unit of Ramon Magsaysay in Zambales, which first served as a supply and intelligence unit. After the surrender in May 1942, Magsaysay and his unit formed a guerrilla force which grew to a 10,000-man force by the end of the war. Another was the Hunters ROTC which operated in the Southern Luzon area, mainly near Manila. It was created upon dissolution of the Philippine Military Academy in the beginning days of the war. Cadet Terry Adivoso refused to simply go home as cadets were ordered to do, and began recruiting fighters willing to undertake guerrilla action against the Japanese. This force would later be instrumental, providing intelligence to the liberating forces led by General Douglas MacArthur, and took an active role in numerous battles, such as the Raid at Los Baños. When war broke out in the Philippines, some 300 Philippine Military Academy and ROTC cadets, unable to join the USAFFE units because of their youth, banded together in a common desire to contribute to the war effort throughout the Bataan campaign. The Hunters originally conducted operations with another guerrilla group known as the Marking Guerrillas, with whom they went about liquidating Japanese spies. Led by Miguel Ver, a PMA cadet, the Hunters raided the enemy-occupied Union College in Manila and seized 130 Enfield rifles.

Also, before being proven false in 1985 by the United States Military, Philippine President Ferdinand Marcos claimed that he had commanded a 9,000-strong guerrilla force known as the Maharlika Unit. Marcos also used maharlika as his personal pseudonym; depicting himself as a bemedalled anti-Japanese Filipino guerrilla fighter during World War II. Marcos told exaggerated tales and exploits of himself fighting the Japanese in his self-published autobiography Marcos of the Philippines which was proven to be fiction. His father, Mariano Marcos, did however collaborate with the Japanese and was executed by Filipino guerrillas in April 1945 under the command of Colonel George Barnett, and Ferdinand himself was accused of being a collaborator as well.

In July 1942, South West Pacific Area (SWPA) became aware of the resistance movements forming in occupied Philippines through attempted radio communications to Allies outside of the Philippines; by late 1942, couriers had made it to Australia confirming the existence of the resistance. By December 1942, SWPA sent Captain Jesús A. Villamor to the Philippines to make contact with guerrilla organizations, eventually developing extensive intelligence networks including contacts within the Second Republic Government. A few months later SWPA sent Lieutenant Commander Chick Parsons, who returned to the Philippines in early 1943, vetting guerrilla leaders and established communications and supply for them with SWPA. Through the Allied Intelligence Bureau's Philippine Regional Section, SWPA sent operatives and equipment into the Philippines to supply and assist guerrilla organizations, often by submarine. The large cruiser submarines USS Narwhal and USS Nautilus, with a high capacity for personnel and supplies, proved especially useful in supporting the guerrillas. Beginning in mid-1943, the assistance to the guerrillas in the Philippines became more organized, with the formation of the 5217th Reconnaissance Battalion, which was largely composed of volunteer Filipino Americans from the 1st and 2nd Filipino Infantry Regiments, which were established and organized in California.