He studied medicine from 1926 to 1931 at the Faculdade de Medicina da Universidade do Brasil (presently the Federal University of Rio de Janeiro. While a student he worked at Manguinhos, where the Instituto Oswaldo Cruz was founded by the eminent physician Dr. Oswaldo Cruz (1872–1917) and where his father worked, as well as at a hospital in Lassance, state of Minas Gerais, where his father had discovered Chagas disease. After graduation he went to become a director of this hospital during 1932. But what he really liked to do was biomedical research, following the example of his father and colleagues, so in the next years he worked with several leaders in the field of physiology, such as Miguel Osório de Almeida (1890-1952) and José Carneiro Felippe. One year after graduation, he accepted a teaching post as assistant professor at the Medical School, in the chair of Biological Physics. With the death of its incumbent, Prof. Lafayette Rodrigues Pereira, he became its chairman and full professor.
Feeling the need to specialize further in neurophysiology, Dr. Chagas Filho travelled to France, where he worked with René Wurmser and Alfred Fessard, in Paris, and to England, where he worked with A.V. Hill (1886–1977). Returning to Brazil, he established a Laboratory of Biophysics at the Medical School and assembled a group of students and researchers. In 1945 he achieved the elevation of the Laboratory to the Biophysics Institute, which in a short time became one of the most important and excellent research centers in Brazil. He was its director for a long time, as well as the dean of the Medical School. The Institute presently bears his name. Dr. Carlos Chagas Filho retired in 1980, but continued to work steadfastly almost until his death, at 89 years of age.
As an educator, Dr. Chagas Filho left a very important influence on biomedical research in Brazil, through his many scientific disciples and colleagues at the Biophysics Institute, many of whom went to became leaders themselves in neurophysiology, such as Hertha Meyer, Hiss Martins Ferreira, Eduardo Oswaldo Cruz Filho, Ricardo Gattass, Aristides Azevedo Pacheco Leão, Eduardo Penna Franca, Gustavo de Oliveira Castro, Darcy Fontoura de Almeida, Antonio Paes de Carvalho, Carlos Guinle da Rocha Miranda, Romualdo José do Carmo and several others. It was during the initial years of the Institute, also, that Rita Levi-Montalcini (1901-), then a young researcher of Jewish descent who had to escape fascism, worked towards her important discoveries on neurotrophic factors, supported by Carlos Chagas Filho. She later went to receive the Nobel Prize of Physiology and Medicine.
He published several books, including an autobiography, a biographical memoir about his father and more than 100 scientific papers.
In 1972, he was appointed by Pope Paul VI to the presidency of the Pontifical Academy of Sciences, which he occupied until 1989. During his tenure, he was distinguished with the historical task of rehabilitating Galileo Galilei by the Roman Catholic Church and with coordinating a study of the historical and scientific validity of the Turin shroud. He was deeply religious but sought to reconcile science and religion as best as possible. Thus, he led the Academy of Sciences through a number of important meetings and publications, examining controversial issues such as the brain and conscience, and attracting great scientific personalities to the Academy, including a number of Nobel awardees.
In Brazil he was a member, vice-president and president of the Brazilian Academy of Sciences (1941–2000) and member of the Brazilian Academy of Letters (1974–2000), a member of the National Research Council and one of the founders and member of the Brazilian Society for the Advancement of Science.
Carlos Chagas Filho was awarded with 16 titles of Honoris Causa Doctor in many national and foreign universities, and 19 decorations, including that of Légion d'Honneur (1979) and the Brazilian Order of Scientific Merit. He was a member of the French Académie des Sciences and Académie National de Médicine, Academia das Ciências de Lisboa, American Academy of Arts and Sciences, American Philosophical Academy, Royal Academy of Belgium, Romenian Academy of Sciences and the International Academy of the History of Sciences.
Among his many scientific awards, he received the Moinho Santista Science Prize (1960); the Prêmio Álvaro Alberto para a Ciência e Tecnologia (1988); and the Prix mondial Cino Del Duca, by the Fondation Simone et Cino Del Duca, France (1989)