He stayed at the University of Iowa for the duration of the 2006 spring semester and officially assumed the Cornell presidency on July 1, 2006.

Skorton pledged to end hazing in the fraternity and sorority system, and wrote an op-ed on the topic in The New York Times.

[24] The barriers were removed in favor of nets that were installed under each major bridge - a historically common place for suicides at Cornell.

[27] In December 2018, the Smithsonian announced[28] that Skorton would be leaving his position in June 2019 to become president and CEO of the Association of American Medical Colleges.

Lonnie Bunch, director of the African American History Museum, succeeded Skorton and became the 14th Secretary on June 16, 2019.

[29] David Skorton is president and CEO of the Association of American Medical Colleges (AAMC), a non-profit organization based in Washington, D.C.[30] When he assumed the presidency of the AAMC, Skorton said he would focus on three challenges: diversity, equity, and inclusion (DEI); mental health and substance use disorders; and access and affordability of care.

[30] In November 2019, he wrote an op-ed for The Washington Post that called for the Supreme Court to consider the negative effects that would result from deporting the approximately 27,000 healthcare workers with DACA status.

[30] In June 2020, when the Supreme Court ruled that DACA could not be ended, Skorton praised the decision, stating that the AAMC was appreciative that the ruling allowed those healthcare workers to continue providing care throughout the U.S.[31] In January 2020, he issued a call to action to medical schools as the first step in an initiative to improve equity in pay, promotion, and other areas for women.

[30] In December 2019, the AAMC released data that showed that, for the first time in history, women comprise the majority of enrolled medical students in the U.S. at 50.5%.

[34] After less than a year in office, Skorton was responsible for leading the AAMC's 171 medical schools and over 400 teaching hospitals and systems through the initial phases of the coronavirus pandemic.

[35] In July 2020, Skorton joined other executives at the AAMC in issuing a statement in support of Dr. Anthony Fauci, the top federal infectious disease official.

[38] In August 2020, Skorton released a statement that the AAMC was alarmed at changes to the CDC’s testing guidelines for individuals not showing symptoms of the disease.

He was also co-host of a weekly program, "As Night Falls - Latin Jazz," on KSUI FM, the University of Iowa's public radio station.