He served in the Philippines attached to the 45th Infantry (Philippine Scouts), evaded capture in the spring of 1942, and organized a guerrilla regiment in the Central Plains of the northern island of Luzon. He was promoted to Major by war's end, age 28, and was awarded the Distinguished Service Cross by General Douglas MacArthur. Lapham was the third person, after President Franklin Delano Roosevelt and MacArthur, to receive the Philippine Legion of Honor.
A graduate of the University of Iowa, Lapham worked for the Chicago branch of the Burroughs Corporation when, as a 2nd lieutenant of infantry in the US Officers Reserve Corps, he was assigned to active duty in the Philippines and sailed from San Francisco on June 5, 1941.
After MacArthur was evacuated to Australia, Gen. Jonathan Wainwright was given command of the Philippine defense force. As talk of surrender began, Lapham sneaked through the lines. In his 1996 book, Lapham’s Raiders: Guerrillas in the Philippines, 1942–45, he explained why he headed to the jungles to fight: "Somehow, I didn’t like the idea of surrendering. I felt I had better chances on the outside than in a Japanese prison camp."
He initially was assigned to Lt. Col. Claude Thorp's infiltration party, where he was placed in charge of recruiting guerrillas in Western Tarlac and Pangasinan provinces. When Thorp was captured, Lapham kept his own guerrilla organization intact and independent, later joined by Ray Hunt, Al Hendrickson, Henry A. Mucci and others. When Major Russell W. Volckmann claimed command over him, Lapham told MacArthur's headquarters that he reported to Major Bernard Anderson's Kalayaan Command.
The estimated 10,000 Filipinos under Lapham's command became known as the Luzon Guerrilla Armed Forces (LGAF), more informally Lapham’s Raiders. They launched a guerrilla campaign of freedom fighting and sabotage against the occupying Japanese soldiers, yomping large amounts of equipment by hand over rugged terrain. The Japanese army put a $1 million bounty on his head.
Lapham is credited for bringing the perilous situation of the 500 allied POWs and internees remaining in the Cabanatuan POW camp to the attention of the American forces then fighting their way across Luzon towards Manila in January 1945. The POWs, captured after the fall of Corregidor and Bataan in 1942, were those the Japanese had not to be shipped to Japan as they were considered too ill or unfit. Lapham's was concerned the POWs would be executed before the allied forces liberated the camp. His concerns were well justified given the August 1944 Japanese War Ministry directive to commandants of POW camps outlining the final disposition of prisoners (known as the "August 1 Kill-All Order") and the killing of 144 American POWs by the Japanese at Palawan, Philippines on 14 Dec 1944. Lapham's efforts lead to the mission by 121 members of the US Army's 6th Ranger Battalion to march 30 miles behind enemy lines, eliminate the Japanese forces securing the camp, liberate its 513 prisoners and return them to American lines. This raid is described in Hampton Sides book, "Ghost Soldiers."