Abraham Flexner, younger brother of the medical researcher Simon Flexner, graduated from Johns Hopkins University at age 19. Nineteen years later he did graduate studies at Harvard University and at the University of Berlin. After graduating from Johns Hopkins, Flexner returned to Louisville and founded a private school in which to test his ideas about education. He believed that education should be marked by small classes, personal attention, and hands-on teaching.

Between 1912 to 1925, Flexner served on the Rockefeller Foundation's General Education Board, and after 1917 was its secretary. With the help of the Board, he founded another experimental school, the Lincoln School, which opened in 1917, in cooperation with the faculty at Teachers College of Columbia University. In 1908, Flexner published his first book, The American College. Strongly critical of many aspects American higher education, it was especially critical of the university lecture as a method of instruction. According to Flexner, lectures enabled colleges to "handle cheaply by wholesale a large body of students that would be otherwise unmanageable and thus give the lecturer time for research."

Flexner's book attracted the attention of Henry Pritchett, President of the Carnegie Foundation, who was looking for someone to lead a series of studies of professional education. Although Flexner had never set foot inside a medical school, Flexner was Pritchett's first choice to lead a study of American medical education. Thus Flexner joined the research staff at the Carnegie Foundation in 1908. Two years later, he published the Flexner Report, which examined the state of American medical education and led to far-reaching reforms in the way doctors were trained.

With Louis Bamberger, Flexner founded the Institute for Advanced Study in Princeton, heading it from 1930 to 1939 and overseeing a faculty that included Kurt Gdel, Albert Ienstein, and John von Neumann. During his time there, Flexner helped to bring over many European scientists who would have likely suffered prosecution at the hands of the rising Nazi government. Flexner penned the letter inviting Albert Einstein to the Institute and to the United States.