She served during World War II as first director of the WAVES (Women Accepted for Volunteer Emergency Service) in the United States Navy.

She was a U.S. delegate to the United Nations Education, Scientific, and Cultural Organization (UNESCO) and was co-chair of President John F. Kennedy's Women's Committee for Civil Rights.

Her Presbyterian family emphasized and helped to nurture a strong faith and a high expectation of achievement which influenced her religious work later on.

[5] Unlike her female contemporaries, McAfee's significance to the church, as well as her service to her country, did not come through women's organizations, Christian education, or missionary work.

[3] During World War II, McAfee took a leave of absence from Wellesley to direct the newly formed WAVES, a force that eventually numbered more than 80,000 women, both enlisted and officer.

[7] McAfee was commissioned as a lieutenant commander the following week, on 3 August, and quickly set down rules for enlisted women, including that they use only enough make-up "to look human".

These efforts resulted in Public Law 183, effective on 9 November 1943, which entitled all Women's Reserve personnel the allowances and benefits available to men.

She told the council, "that the secular institutions need to be supplemented by a virile church, alert to its unique mission to keep man conscious of his relation to the loving, judging, living God.

[16] While holding this office with the National Council of Churches, she also sat on the boards of NBC and RCA in order to develop religious programming.