The Clark Cemetery was formed between 1947 and 1950 by moving the headstones/markers and remains from at least four other U.S. military cemeteries (Fort Stotsenburg 1 & 2, Fort McKinley, and Sangley Point naval cemetery) to the new 20.365 acre, 12,000 plot cemetery located just inside the main gate of Clark Air Base. All WWII dead were moved to the American Cemetery in Manila.

The cemetery contains the remains of U.S. veterans from the USA, USN, USMC, USCG, USAF, Philippine Scouts (PS) and their dependents. Some, but not all, were veterans of the Spanish/American, Philippine Insurrection, WWI, WWII (died after the war), Korean, Vietnam, and Iraq wars. The largest category interred are civilian, mostly U.S. and Filipino and their dependents, all of whom worked for the U.S. Government. In addition, nationals from France, Spain, Canada, Japan, China, Vietnam and India are buried there.

The earliest recorded burial is Santiago Belona, Pvt, PS, DOD: Jan 13, 1900. There are no records, but it is probable that this individual was moved from either Fort Stotsenburg 1 or 2. There are 8,649 individuals buried in the cemetery as of December 31, 2010.

Dual flags have flown over the cemetery since March 1984. A special waiver was given to the provisions of the 1979 revised MBA to allow the U.S. flag to be displayed. This revision was secured from the Philippine government at the request of the Commander, 13th Air Force, Major General Burns. From 1979-1984, only one U.S. flag had been allowed to be flown on Clark Air Base…the one located immediately in front of 13th Air Force headquarters.

The Veterans of Foreign Wars Post 2485 in Angeles City supported and maintained the cemetery between 1994 and 2013. In December 2013, operational control of the cemetery was assumed by the U.S. American Battle Monuments Commission, making Clark ABMC's 25th cemetery.