After the war, Lay transitioned to the State Department as a management analyst, working under the special assistant responsible for research and intelligence.[1] He worked at the State Department for two months, before being selected for a new assignment.[1]
In 1946, Lay was selected by Admiral Sidney Souers to become the Secretary of the Intelligence Advisory Board (IAB) within the Central Intelligence Group (CIG) during its brief existence.[2] In this capacity, he was responsible for coordinating meetings and facilitating communication among the board members, who were the intelligence chiefs of the Departments of State, War, Navy, and the Air Force.[2] The IAB played a crucial role in advising the Director of Central Intelligence (DCI) on matters of national intelligence.[3]
Lay's role as Executive Secretary involved organizing agendas, documenting discussions, and ensuring that directives and decisions were effectively communicated and implemented across the various intelligence agencies. His efforts contributed to the foundational coordination and integration of U.S. intelligence activities during the immediate post-World War II period.[2]
The National Security Act of 1947 changed the structure of the intelligence community. Following the transition of the Central Intelligence Group into the Central Intelligence Agency (CIA), and the transition of the NIA into the National Security Council (NSC), Lay became the Assistant Executive Secretary of the NSC, with Souers becoming its Executive Secretary.[1]
In 1950, with Souers announcing his retirement, Lay became the Executive Secretary of the NSC, where he was instrumental in shaping national security policies during the early years of the Cold War. In this job, he was responsible for coordinating national security policies and decisions.[1] His duties as the Executive Secretary also involved his being primarily responsible for the permanent staff of the NSC.[4] A portrait of him in this capacity is archived at the Harry S. Truman Library.[5]
However, in The Journal of American History, Anna Kasten Nelson wrote that Lay did little to soothe the tensions that had formed at the NSC between Louis A. Johnson and Dean Acheson, who were at loggerheads over intelligence policy. Nelson wrote:
"Johnson's dislike of Acheson was so great that relations between the two departments hardly extended beyond the most basic liaison. The two secretaries rarely exchanged a word. Unfortunately, as the relationship between Johnson and Acheson disintegrated, the process was further weakened by the departure of Souers in January 1950. James S. Lay, Jr., who replaced him as executive secretary, was a competent director of the secretariat's functions but regarded himself as a servant of the NSC rather than as a staff assistant to the president. He was either unwilling or unable to assume the tasks of coordinating information and smoothing relationships that were performed by Souers. The situation was further complicated by the fact that Souers remained as a consultant to the president. His services were intermittent in that role, but his presence precluded anyone else from stepping into the vacuum."[6]
In 1964, while Lay was serving on the United States Intelligence Board, he was awarded the National Civil Service League (NCSL) Career Service Award.[7]
In 1971, Lay officially retired, but continued to work as a consultant to the President's Intelligence Advisory Board until 1977.[1]