The outbreak of the war in the Pacific cut short the activities of the Fraternity, which remained inactive through the dark years of the Japanese occupation. However, upon the reopening of classes in the University of the Philippines, steps were taken to reactive the Fraternity. Brother Juan Z. Bagasan of the Mother Alpha chapter in Washington brought with him the authority from Dr. Macy Skinner, retired International President of the Fraternity, to reactive the Philippine Alpha Chapter. With him as Chairman, together with Bros. Pablo Mabbun, Santiago de la Cruz, Manual Rustia, Cirilo Asperilla, Laureano Ma. Rivera. Salvador Gonzales, Hernando Munoz, and Dominador Torres, committee was formed to take charge of the reactivation drive.

On March 6, 1947, the Philippine Alpha Chapter was reactiviated with Dominador Torres elected as Governor and Prof. Pablo N. Mabbun as the adviser. With this as a headstart, the Fraternity resumed its activities with a post-war reunion at the Rotary Room of the Manila Hotel with Bro. Carlos P. Rumulo as the principal speaker. A series of cocktail conferences followed and the Fraternity was off to a flying start. The departure of Prof. Mabbun for Japan as head of the Philippine Trade Mission occasioned the designation of a new adviser in the person of Prof. Bienvenido Y. Dizon.

Perhaps the first most important post-war activity of Pan Xenia was its role in the ECAFE, which was held in Baguio where the Philippine delegation was composed of Pan Xenians. By then, several men were initiated to the Fraternity to replace those who had perished during the war. Others too were elevated to higher ranks of membership in the Fraternity, as was Gil J. Puyat who reached the peak of honorary membership having started as an active member. Miguel S. Cuaderno Sr., who was then Secretary of Finance, became the latest addition to the ranks of honorary members.

On February 1948, a reception and dinner-dance was held to celebrate a successful year of revival with Ambassador O'neal and Carlos P. Rumulo as guests of honor. Pan Xenians, young and old, took time out from their serious affairs and activities to relax and refresh their fraternal ties. A necrological service for the deceased Pan Xenians marked the close of the Fraternity's first post-war year of activities. .