With a Bishop Museum fellowship, she conducted her first field research in 1933, studying traditional exchange and settlement patterns in the Lau Islands of southern Fiji.
In 1938, the Naval governor of Guam requested that Thompson serve as his consultant on Native Affairs to suggest improvements to the educational and welfare systems for CHamorus.
[1] She conducted a "six-month field study of the native Chamorro population, their daily life, land use customs, changing economy, schooling, cultural values, and local government under American military rule since 1899.
[1] Thompson held a research position in the Committee on Human Development at the University of Chicago in 1941 when she received a grant to serve as the Coordinator of the Indian Education, Personality and Administration Project.
The Institute published an opinion piece by Harold L. Ickes immediately after he retired as secretary of the Interior that argued, among other things, that the Navy should not be governing Guam and American Samoa.
[7] As a result of Thompson's political activism on behalf of CHamoru self-government, the U.S. military, which controlled travel on and off of Guam, denied her permission to return for many years after the war.
In her speech accepting the 1979 Bronislaw Malinowski Award from the Society for Applied Anthropology, Thompson highlighted how the first generation of applied anthropologists advised those trying to make colonialism more efficient, noting that these early anthropologists were "under a certain degree of pressure from the larger society to develop a set of tools for engineering, manipulating, and managing people in small groups and ethnic enclaves toward utilitarian goals superimposed from without.
"[1] Thompson made her first return visit to Guam in 1977, when she was invited to be the keynote speaker for the CHamoru Studies Conference held at George Washington High School.
She returned again in April 1987 to give the keynote speech, titled "Talking Stones," to the University of Guam's Annual College of Arts and Sciences Research Conference.
In 1991, the Richard F. Taitano Micronesian Area Research Center (MARC) of the University of Guam hosted a reception at the Bishop Museum to honor Thompson on the publication of her autobiography, Beyond The Dream.