Though she began her career with a 4-year stint as an instructor at Yale, Aberle spent most of her career working in Native American areas. She was employed by the Bureau of Indian Affairs from 1935 to 1944, then took a position with National Research Council until 1949, and from 1949 to 1954 at the University of New Mexico. In 1948, her first major book was published, which placed Aberle as a strong proponent of Pueblo land rights.
She and Gerty Cori were the first women appointed to the National Science Board by President Harry Truman in 1951. Aberle remained a member until 1957. She worked for the Bernalillo County Indian Hospital as its chief nutritionist until 1966 when she returned to the University of New Mexico as a professor of psychiatry, a position she maintained until her 1970 retirement.
Aberle spent much of her career working on committees for land allocation and health. She was a member of the upper Rio Grande drainage basin committee, the health committee of the All Indian Pueblo Council, the New Mexico Nutrition Committee, the White House Conference on Children in Democracy, the Committee of Maternal and Infant Mortality, Planned Parenthood, and was the chair of the board of directors for the Southwest Field Training School for Federal Service and the Commission on Rights, Liberties, and Responsibilities of American Indians.