The assassination of President Kennedy on November 22, 1963, shook the Joint Chiefs as much as the country at large and left a void that the new President, Lyndon B. Johnson, moved quickly to fill. To reassure the Nation and to promote stability, he pledged continuity between his administration and Kennedy’s. "I felt from the very first day in office,” he recalled, "that I had to carry on for President Kennedy. I considered myself the caretaker of both his people and his policies.” One of those who stayed on was Secretary of Defense Robert McNamara. The dominant figure at the Pentagon before Kennedy’s death, McNamara would exercise even more power and authority during Johnson’s Presidency

For an organization that did not adapt easily to change, John F. Kennedy’s Presidency was one of the most formidable challenges ever to face the Joint Chiefs of Staff. Representing youth, enthusiasm, and fresh ideas, Kennedy entered the White House in January 1961 committed to blazing a "New Frontier” in science, space, and the "unresolved problems of peace and war.” As a Senator and Presidential candidate, Kennedy had been highly critical of the Eisenhower administration’s defense program, faulting it for allowing the country to lag behind the Soviet Union in missile development and for failing to develop a credible conventional alternative to nuclear war. "We have been driving ourselves into a corner,” Kennedy insisted, "where the only choice is all or nothing at all, world devastation or submission—a choice that necessarily causes us to hesitate on the brink and leaves the initiative in the hands of our enemies.” Instead of threatening an all-out nuclear response, Kennedy advocated graduated levels of conflict tailored to the needs of the situation and the degree of provocation, in line with the "flexible response” doctrine put forward by retired General Maxwell Taylor, former Secretary of State Dean Acheson, and others.

On October 4, 1957, the Soviet Union stunned the world by sending an artificial satellite, "Sputnik I,” into orbit around the Earth. This achievement was the first of its kind and followed the successful launch of a Soviet multistage intercontinental ballistic missile (ICBM) the previous August. It would be more than a year before the United States successfully tested an ICBM. Suggesting a higher level of Soviet technological development than previously assumed, Sputnik I and the Soviet ICBM cast doubt on a key assumption that had shaped U.S. national security policy since World War II—that America’s supremacy in science and technology gave it a decisive edge over the Soviet Union. Not since the Soviets tested their first atomic bomb in 1949 had the United States seemed so unprepared and vulnerable. According to James R. Killian, Jr., President Eisenhower’s assistant for science and technology, Sputnik I "created a crisis of confidence that swept the country like a windblown forest fire.”