Lee was called as a member of the Quorum of the Twelve Apostles on 6 April 1941. As he looked around the upper room of the Salt Lake Temple where the quorum held its meetings, he discovered that every man there was at least twenty years his senior. He thought of himself as a seedling among giant redwoods, causing his tutor and friend, J. Reuben Clark, Jr., to refer to him affectionately as "Kid."
Early in his apostleship, Elder Lee served on a committee along with two senior members of the Twelve with the assignment to simplify church organization and functions. Through two decades Lee studied the subject and prepared proposals, but he learned patience while awaiting the right time to implement his reorganizational concepts. The time for action finally arrived twenty years later when, under the direction of LDS Church President David O. McKay, the Correlation Program was introduced, with Lee as chairman, innovator, and organizational scholar. Through this committee, a complete restructuring of the church occurred in the 1960s, with auxiliary organizations assigned a supporting role under priesthood direction. A return to simplicity was accomplished, and the home received primary emphasis.