As president, Zimmer pushed for major academic initiatives at Chicago,[6] including increased financial aid for students in the undergraduate College and the elimination of loans from financial aid packages;[7] increased funding for doctoral students, particularly in humanities and social sciences;[8] the University of Chicago's first engineering program, which began as the Institute for Molecular Engineering[9] and is now the Pritzker School of Molecular Engineering; new programs and facilities in the arts;[10] and the establishment of the Becker-Friedman Institute for Research in Economics,[11] the Neubauer Family Collegium for Culture and Society, and the Stevanovich Institute on the Formation of Knowledge.

[18] The University adopted a policy of meeting full financial need of its undergraduate students with no loan expectations, creating the capacity for them to graduate debt-free.

[25] As Zimmer noted in an address to the Chicago Humanities Festival in 2017, the work of faculty and students to confront new and different ideas through education and research "only happens at the highest level in an environment of rigor, questioning, and free and open discourse.

[27] Under Zimmer's guidance, the University of Chicago sent a letter to incoming freshmen in August 2016 telling them that "we do not support so-called trigger warnings, we do not cancel invited speakers because their topics might prove controversial, and we do not condone the creation of intellectual safe spaces where individuals can retreat from ideas and perspectives at odds with their own.

[29] On August 13, 2020, Zimmer announced that he would step down as president at the conclusion of the 2020–2021 academic year and that he would shift to the role of chancellor; he originally had planned to serve through 2022, but acknowledged that brain surgery he had undergone in May 2020 had accelerated his transition.

Much of his work was in the area now known as the "Zimmer Program" which aims to understand the actions of semisimple Lie groups and their discrete subgroups on differentiable manifolds.

[34] In collaboration with François Labourie and Shahar Mozes, cocycle superrigidity ideas were applied to the basic problem of the existence of compact locally homogeneous spaces of certain types.

[37] Zimmer was married to Terese Schwartzman, former director of strategic initiatives for the university's Urban Education Institute, but they separated in September 2009 and later divorced.