Flexner was born in Louisville, Kentucky on November 13, 1866. He was the sixth of nine children born to German Jewish immigrants, Ester and Moritz Flexner. He was the first in his family to complete high school and go on to college. In 1886, at age 19, Flexner completed a Bachelor of Arts in classics at Johns Hopkins University, where he studied for only two years. In 1905, he pursued graduate studies in psychology at Harvard University, and at the University of Berlin. He did not, however, complete work on an advanced degree at either institution.