Jagendorf attended the Bronx High School of Science, and received a bachelor's degree in plant physiology from Cornell in 1948. He completed his doctorate in biophysics at Yale University in 1951 and was a Merck Fellow at the University of California, Los Angeles before joining the faculty at Johns Hopkins in 1953. He returned to Cornell as professor of plant physiology in 1966. In 1981 he became the Liberty Hyde Bailey Professor and from 1997-2017 he was the Liberty Hyde Bailey Professor Emeritus in the Department of Plant Biology. In 1980 he was elected to the National Academy of Sciences and in 2007 he was named one of the first fellows of the American Society of Plant Biology.