He also had a strong sense of service to both the medical community and the wider community it served. Dr. Cooper was an associate dean of the Northwestern Medical School from 1959-1963. He started the "Charter 25" program, which allowed students to begin medical training straight out of high school and become doctors in six rather than eight years. He directed this program and served as a full-time mentor to the program participants from 1960-1968. From 1962-1969, he served on the editorial board for the AAMC's Journal of Medical Education, was a member of the Illinois Board of Public Health Advisors, and was part of the Illinois Legislative Commission on Atomic Energy. Dr. Cooper became even more involved with the AAMC and medical education when in 1969 he was asked to become the first president of the Association of American Medical Colleges (AAMC), which up until then had been run by an Executive Director. Dr. Cooper helped bring the AAMC and its role in medical education to the forefront of the public's attention. He moved the AAMC's offices from Evanston, Illinois to Washington, D.C. shortly after assuming its presidency, and rapidly established the AAMC and himself as a credible voice for medical education and research. He grew the Association from a small staff in Evanston to a staff of several hundred in Washington, organizing and operating the MCAT test, the AMCAS centralized application service, and conducting leading-edge educational research. He also expanded the AAMC's role from one of a "dean's club" to one that also spoke for medical school faculty, researchers and hospital administrators. He also helped to organize the National Intern and Resident Matching Program. In 1981, he was named by U.S. News & World Report as one of the five most influential people in medicine and health education. Dr. Cooper retired from his position as AAMC president in 1986.
