Born in Shanghai, China, Fischer was educated at the University of Geneva, where, after graduation, he worked as an assistant in the organic chemistry laboratories (1946–47). After spending two years as a research fellow with the Swiss National Foundation (1948–50) he moved to the University of Washington, Seattle, as a Rockefeller Foundation research fellow (1950–53). After a brief spell at the California Institute of Technology in 1953, he was appointed an assistant professor of biochemistry at the University of Washington, subsequently becoming associate professor (1956–61) and professor (1961–90).

Fischer's most acclaimed work was done at Seattle in the 1950s and 1960s in collaboration with the biochemist Edwin Krebs. In 1955–56 the scientists discovered how the enzyme (glycogen phosphorylase) that catalyzes the release of glucose from glycogen in the body is “switched on.” The enzyme receives a phosphate group from ATP (adenosine triphosphate – the body's major energy carrier) in a transfer reaction catalyzed by a second enzyme, which Fischer and Krebs termed a “protein kinase.” They went on to show that glycogen phosphorylase is then switched off by removal of the phosphate group by a further enzyme (called a protein phosphatase). The addition and removal of the phosphate group reversibly changes the shape of the enzyme molecule, thereby switching it between the inactive and active forms.

These findings opened the way to a major new field of research suggesting how enzymes might function in various physiological processes, such as hormone regulatory mechanisms, gene expression, and fertilization of the egg. Their work also had implications for the understanding of certain diseases; for instance, abnormally phosphorylated proteins have been identified in muscular dystrophy and diabetes, while protein kinases may play a significant role in certain cancers and in airway constriction in asthma.

In recognition of his contributions to our understanding of enzymes Fischer was awarded the 1992 Nobel Prize for physiology or medicine, which he shared with his long-time coworker, Krebs.