In 1994 Lewis coauthored the "comprehensive" Report on the Structure of Harvard College, and in 1995 he was appointed dean of Harvard College, responsible for the nonacademic aspects of undergraduate life.
In that capacity he oversaw a number of sometimes-controversial policy changes, including changes to the handling of allegations of sexual assault, reorganization of the college's public-service programs, a crackdown on underage alcohol use, and random assignment of students to upperclass houses (countering the social segregation found under the prior system of assignment according to student preference).

He also pressed improvements to advising and health care.

A colleague has said that Lewis "reshaped undergraduate life more powerfully than anyone else in recent memory."

After the 2001 inauguration of Harvard University's twenty-seventh president, Lawrence Summers, Lewis and Summers came into conflict over the direction of the College and its educational philosophy.
Lewis, for example, emphasized the importance of extracurricular pursuits, advising incoming freshmen that "flexibility in your schedule, unstructured time in your day, and evenings spent with your friends rather than your books are all, in a larger sense, essential for your education", while Summers complained of an insufficiently intellectual "Camp Harvard" and admonished students that "You are here to work, and your business here is to learn."
After Lewis issued what The Harvard Crimson called "a scathing indictment of the view that increasing intellectual rigor ought to be the [College's] priority" – pointing out that prospective employers show less interest in grades than in personal qualities built outside the classroom – he was peremptorily removed as dean in March 2003.

Lewis continued to teach throughout his time as dean.
In 2015 he served as interim Dean of the Harvard School of Engineering and Applied Sciences.
In 1994 Lewis coauthored the "comprehensive" Report on the Structure of Harvard College, and in 1995 he was appointed dean of Harvard College, responsible for the nonacademic aspects of undergraduate life. In that capacity he oversaw a number of sometimes-controversial policy changes, including changes to the handling of allegations of sexual assault, reorganization of the college's public-service programs, a crackdown on underage alcohol use, and random assignment of students to upperclass houses (countering the social segregation found under the prior system of assignment according to student preference).
He also pressed improvements to advising and health care.
A colleague has said that Lewis "reshaped undergraduate life more powerfully than anyone else in recent memory."
After the 2001 inauguration of Harvard University's twenty-seventh president, Lawrence Summers, Lewis and Summers came into conflict over the direction of the College and its educational philosophy. Lewis, for example, emphasized the importance of extracurricular pursuits, advising incoming freshmen that "flexibility in your schedule, unstructured time in your day, and evenings spent with your friends rather than your books are all, in a larger sense, essential for your education", while Summers complained of an insufficiently intellectual "Camp Harvard" and admonished students that "You are here to work, and your business here is to learn." After Lewis issued what The Harvard Crimson called "a scathing indictment of the view that increasing intellectual rigor ought to be the [College's] priority" – pointing out that prospective employers show less interest in grades than in personal qualities built outside the classroom – he was peremptorily removed as dean in March 2003.
Lewis continued to teach throughout his time as dean. In 2015 he served as interim Dean of the Harvard School of Engineering and Applied Sciences.
Harry R. Lewis