In September 1950, he entered the University of Illinois for graduate training in nuclear physics and received a master of science degree in 1952. He earned his doctorate degree in physics in 1954 after completing an experimental thesis on high energy photonuclear reactions. General Allen then was assigned to the U.S. Atomic Energy Commission's Los Alamos Scientific Laboratory in New Mexico as a physicist in the Test Division, where he became friends with bomb designer Ted Taylor. He conducted experiments in several of the nuclear test series. These experiments related to the physics of thermonuclear weapons design and to the effects of high altitude nuclear explosions for ballistic missile defense.
From June 1957 to December 1961, General Allen was assigned to Kirtland Air Force Base, New Mexico, as science adviser to the Physics Division of the Air Force Special Weapons Center. He specialized in the military effects of high altitude nuclear explosions and participated in several weapon test series. He was scientific director of a major experiment that utilized a large series of high altitude rockets to measure the characteristics of electrons trapped in the geomagnetic field after an exoatmospheric nuclear burst.
He was assigned in December 1961, to the Office of the Secretary of Defense, Space Technology Office in the Directorate of Research and Engineering, Washington, D.C. From June 1965 to February 1973, he was assigned to the Office of the Secretary of the Air Force, initially in Los Angeles as deputy director for advanced plans in the Directorate of Special Projects. He moved to The Pentagon in June 1968 as deputy director of space systems and in June 1969 became director. He returned to Los Angeles in September 1970 as assistant to the director of special projects and in April 1971 became director of special projects, with additional duty as deputy commander for satellite programs, Space and Missile Systems Organization.
After serving briefly as chief of staff for Air Force Systems Command at Andrews Air Force Base, Maryland, General Allen was appointed in March 1973 as deputy to the Director of Central Intelligence for the Intelligence Community in Washington, D.C. In August 1973, he became director, National Security Agency and chief, Central Security Service at Fort George G. Meade, Maryland. Allen's tenure as NSA director was noteworthy in that he became the first NSA director to ever testify publicly before Congress. In August 1977, he was named commander of Air Force Systems Command.
Allen served as the vice chief of staff, U.S. Air Force from April 1978 until he became Chief of Staff of the United States Air Force in July 1978. His nomination was unusual in that he had never served an overseas or a combat assignment, and most of his positions were in highly specialized activities rather than in the usual command structure of the Air Force.
Allen was awarded the 1999 Distinguished Graduate Award of the Association of Graduates, the alumni association of West Point graduates.