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. The Women's Reserve (WR) was created when President Roosevelt signed the authorizing legislation into law on July 30, 1942. McAfee was commissioned as a lieutenant commander the following week, on August 3, and quickly set down rules for enlisted women, including that they use only enough make-up "to look human". With others, she campaigned for WAVES to have the same pay and benefits as their male counterparts. These efforts resulted in Public Law 183, effective on November 9, 1943, which entitled all WR personnel the allowances and benefits available to men. It also provided for one captain in the Women's Reserve; Lieutenant Commander McAfee was promoted to captain later that same month. She succeeded in integrating women of color into the U.S. Naval Reserve Officer Corps and enabled them to serve in many areas and capacities while their male counterparts were limited to serving as cooks and bakers. She ensured that women of color would be treated like any of the other WAVES and assigned as officers in various companies. During the peak of World War II, Captain McAfee commanded 82,000 women.