In 1991, Daugherty was invited to join the composition faculty at the University of Michigan School of Music (Ann Arbor). He replaced Leslie Bassett, who retired. Daugherty was co-chair of the composition department with composer William Bolcom from 1998–2001, and chair of the department from 2002–06. At the University of Michigan, Daugherty mentored many young composers, including Clarice Assad, Derek Bermel, Gabriela Lena Frank, Kristin Kuster, David T. Little, Joel Puckett, Andrea Reinkemeyer, Arlene Sierra, D. J. Sparr and Roger Zare. Daugherty has organized residencies of guest composers with performances of their music, including Louis Andriessen, Michael Colgrass, Michael Torke, Joan Tower, Betsy Jolas and György Ligeti. He has also composed new works, including "Niagara Falls" (1997) and "Bells for Stokowski" (2002), for the University of Michigan Symphony Band and its two most recent conductors, H. Robert Reynolds and Michael Haithcock.