In 1950, McAfee became a vice-president at large of the National Council of Churches, upon its founding. She had previously been serving as the first female vice-president of the Federal Council of Churches, which had been working to merge eight interdenominational boards to form the National Council. 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. She would later become the president of the American Board of Commissioners for Foreign Missions.