When Robert Freeman left the Eastman School of Music, James Undercofler became acting director and then was appointed director in 1997. It was during his nine-year tenure that the title of the school's administrative leader was changed from director to dean. Plans to do so had been discussed at least as early as the mid-1960s in an effort to bring the title into conformity with the other schools and colleges of the university. Somehow a decision was consistently deferred, but after about three decades of periodic consideration, it was announced that the leader of the Eastman School of Music would thereafter be known as the dean rather than the director. Undercofler's resignation in 2006 to accept an offer to become chief executive officer of the Philadelphia Orchestra led to the appointment of Jamal Rossi as interim dean during the period 2006–7. Rossi had come to the Eastman School in 2005 to become senior associate dean for academic affairs. Prior to his appointment at Eastman he had served as dean of the School of Music at the University of South Carolina.

In 2007 Douglas Lowry accepted an appointment as the new dean of the Eastman School. He had previously served for seven years as dean and the Thomas James Kelly Professor of Music at the University of Cincinnati College-Conservatory of Music. Lowry led the Eastman School of Music with great distinction until his resignation on September 23, 2013, for reasons of health. He died nine days later at age 62, much mourned by faculty, staff, and students at the Eastman School for whom he had been such an inspiring and compassionate friend and leader. Once again Jamal Rossi was called upon to be the school's interim dean and served in that capacity until he was selected as Lowry's successor in 2014. The history of the school during these years will need to be told in detail at some point in the future, but it deserves to be related at least in summary fashion at this time.

Among new initiatives were several that represented a significant broadening of the school's commitment to the education of the Rochester community, with aims of expanding the understanding and appreciation of music and creating a larger and more knowledgeable audience for music.”