Upon graduation from Holy Cross, Mullaney enlisted in the United States Marine Corps with the 4th Marine Division as a sergeant. He ended the war as a commissioned first lieutenant, having served in Guam and Tinian. He returned to active duty in 1950, at the onset of the Korean War. He was first injured during the recapture of Seoul. He was injured a second time during the Chosin Reservoir campaign. On November 27, 1950, he was awarded his third Purple Heart for an injury at Chosin that would end his military career. He spent the better part of the following year recovering at Chelsea Naval Hospital. His military decorations included three Purple Hearts, Silver Star and Bronze Star.