Carrel received his medical degree from the university in his native city of Lyons in 1900. In 1902 he started to investigate techniques for joining (suturing) blood vessels end to end. He continued his work at the University of Chicago (1904) and later (1906) at the Rockefeller Institute for Medical Research, New York. Carrel's techniques, which minimized tissue damage and infection and reduced the risk of blood clots, were a major advance in vascular surgery and paved the way for the replacement and transplantation of organs. In recognition of this work, Carrel was awarded the 1912 Nobel Prize for physiology or medicine.

During World War I, Carrel served in the French army. With the chemist Henry Dakin, he devised the Carrel–Dakin antiseptic for deep wounds. Returning to the Rockefeller Institute after the war, Carrel turned his attention to methods of keeping tissues and organs alive outside the body. He maintained chick embryo heart tissue for many years on artificial nutrient solutions and with the aviator Charles Lindbergh he devised a so-called artificial heart that could pump physiological fluids through large organs, such as the heart or kidneys.

In Man, the Unknown (1935), Carrel published his controversial views about the possible role of science in organizing and improving society along rather authoritarian lines. During World War II he founded and directed the Carrel Foundation for the Study of Human Problems under the Vichy government, in Paris. Following the Allied liberation, Carrel faced charges of collaboration but died before a trial was arranged.