In 1985, Hockfield joined the faculty of Yale University. She received tenure in 1991 and became a full professor of neurobiology in 1994; soon thereafter she began to take on positions of administrative leadership. From 1998 to 2002, she served as Dean of the Graduate School of Arts and Sciences, with oversight of 70 graduate programs. Over the course of her deanship, the number of applicants to the graduate school doubled while graduate student support expanded in many dimensions, including healthcare, career counseling, fellowships, and opportunities to interact with faculty.