In 1961 Dunnigan left journalism, later becoming one of the first Black women to serve in John F. Kennedy’s administration.
She became an educational consultant to the President's Committee on Equal Employment Opportunity (CEEO) which reviewed federal employment practices, made recommendations for improvements, and developed anti-discrimination rules for government contractors. After Kennedy’s assassination, Dunnigan developed a working relationship with President Lyndon B. Johnson, and reported on discrimination faced by Black Washingtonians and African diplomats, who found it impossible to find housing near their embassies or receive service in restaurants. Dunnigan's experiences as a journalist made her keenly aware that international opinions of the US were severely impacted by Jim Crow.