Soper received a doctorate from the Johns Hopkins School of Public Health.
- In 1927, Soper in Brazil, as administrative head of Rockefeller's regional office, helped conceive and carry out effective campaigns against yellow fever and malaria. He demonstrated that, with proper techniques and meticulous organization, the mosquito vectors of these diseases could be virtually eradicated. He incorporated laboratory analysis into the post-mortem diagnosis of yellow fever--through characteristic changes in liver tissue--and then was able to identify cases of "jungle yellow fever" that occurred even without the Aedes aegypti mosquito, its usual vector. In 1946, Soper was presented with one of the first Lasker Awards "for his splendid organization of eradication campaigns against yellow fever and malaria which have set new standards in the fight to defeat these diseases." He remained a staunch advocate of disease eradication programs ever after.
- Between 1943 and 1946, during World War II, Soper, with personnel from the Rockefeller Foundation and the Allied military health services conducted de-lousing operations in Egypt, Algeria, and Naples, Italy. In the process, they developed an efficient, effective, low-cost typhus control protocol using insecticide powders, including the then-new DDT. 
From 1947 to 1959, Soper was the Director of the Pan American Sanitary Bureau.
Soper won a Lasker Award in 1946. Throughout his career, Fred Soper set new standards for disease control worldwide.
- Killing mosquitoes, Soper always said, was not a matter of knowledge and academic understanding; it was a matter of administration and discipline. 
- Anopheles Gambiae in Brazil, 1930 to 1940, (1943)
- The Organization of Permanent Nation-Wide Anti-Aedes Aegypti Measures in Brazil, (1943)
- Ventures in World Health, (1977)