Miller served as the Master of Saybrook College from 1999 until the autumn of 2008, when she was both appointed as Sterling Professor and named the replacement of Peter Salovey as Dean of Yale College. She was the first woman to hold Yale College's highest office, and served as dean from December 2008 to June 2014. When Yale University President, Richard C. Levin, announced Miller's appointment as dean, he had nothing but praise for her: "Mary is the embodiment of what you look for in a Yale College dean," Levin said in an interview after the official appointment ceremony held in Luce Hall. "She is a magnificent scholar, a devoted teacher and a terrific master." Miller cited a desire to return to academia as her reason for stepping down from the deanship position in 2014.