After graduating from the School of Medicine, Sooy served as a lieutenant in the U.S. Naval Medical Corps in World War II. After the war ended he returned to San Francisco and joined the faculty in 1946. After several years as an associate professor, he rose to full professorship in the School of Medicine in 1961. Dr. Sooy became the Chairman of the Division of Otolaryngology in the Department of Surgery in 1958. He was subsequently named the first Chairman of the Department of Otolaryngology in 1967.
In 1972, Francis A. Sooy became the fourth Chancellor of UCSF, and the first UCSF alumnus Chancellor. He continued his medical practice during his ten-year chancellorship. Some of his accomplishments as Chancellor included making possible the construction of the School of Dentistry building and the Long addition to Moffitt Hospital project, as well as the establishment of the Board of Overseers and the UCSF Foundation.
Sooy had a strong sense of traditions at UCSF. As a result, he established the UCSF Medal, the highest award bestowed by the campus, and in 1982, he inaugurated Founder's Day, an annual celebration of UCSF's contributions to the people of California. The first Founder's Day was dedicated to Dr. Sooy, and during the celebration he was awarded the UCSF Medal. In 1982, Sooy stepped down from as Chancellor and returned to his clinical practice and teaching at UCSF.
Francis A. Sooy was internationally renowned as a surgeon. He is credited with introducing vastly improved methods in the surgical treatment of deafness, and was considered a national expert on tinnitus and Menier's disease. He held memberships in numerous professional societies, including the Pacific Coast Oto-Ophthalmological Society, and of the Society of University Otolaryngologists. He served as president of Collegium Oto-Rhino-Laryngologicum Amicitiae Sacrum, and the president of the American Laryngological, Rhinological, and Otological Society.
Dr. Sooy loved to teach. He produced and aided in the production of teaching films and participated in several television and radio productions. One of his greatest desires was to "build young doctors". He was active in public service, and known for his wise judgment and sincere interest in people.
Francis A. Sooy died on September 12, 1986, while flying his friend's World War II trainer biplane in Rio Vista, Solano County, California.