In 1896, Flexner married a former student of his school, Anne Laziere Crawford. She was a teacher who soon became a successful playwright and children's author. The success of her play "Mrs. Wiggs of the Cabbage Patch" (based on the 1901 novel) funded Flexner's studies at Harvard and his year abroad at European universities. The couple had two daughters Jean and Eleanor. Jean went on to become one of the original employees of the United States Division of Labor Standards. Eleanor Flexner became an independent scholar and pioneer of women's studies.