After the election, the president-elect offered Schlesinger an ambassadorship and Assistant Secretary of State for Cultural Relations before Robert Kennedy proposed that Schlesinger serve as a "sort of roving reporter and troubleshooter." Schlesinger quickly accepted, and on January 30, 1961, he resigned from Harvard and was appointed Special Assistant to the President. He worked primarily on Latin American affairs and as a speechwriter during his tenure in the White House.
In February 1961, Schlesinger was first told of the "Cuba operation," which would eventually become the Bay of Pigs Invasion. He opposed the plan in a memorandum to the president: "at one stroke you would dissipate all the extraordinary good will which has been rising toward the new Administration through the world. It would fix a malevolent image of the new Administration in the minds of millions." He, however, suggested,