Fay Cunningham joined the Manhattan Project in 1944 as a metallurgical engineer at the Massachusetts Institute of Technology, as part of the Special Engineer Detachment. Cunningham and his team of engineers helped to develop a mechanized process for producing crucibles that were used in the reduction of uranium and plutonium.
After the war, Cunningham served as a radiation monitor for the nuclear tests at Bikini Atoll during Operation Crossroads. His job was to survey the radiological damage on navy ships that were positioned around the epicenter of the nuclear explosion. After Operation Crossroads, Cunningham returned to Michigan State and completed his degree in chemical engineering.