The first graduate level courses were offered at the Wisconsin State College at Eau Claire during the summer of 1960, in cooperation with the University of Wisconsin’s College of Education. Only offering these courses in the summer, students could complete two summer sessions at Eau Claire before transferring to UW-Madison (then just the University of Wisconsin) to finish their master’s degree. During the summer of 1960 only seven graduate courses were offered and by the summer of 1963 there were almost thirty courses offered. The graduate program was formally organized in 1963, and by fall 1964 graduate classes were offered during the fall, spring, and summer. The first seven graduate degrees were awarded in 1964, and by 1986 the number of total master’s degrees awarded by the university was well over 2,000.

Over a dozen graduate degree programs would be proposed between 1966 and 1968, with six receiving approvals in 1971: Biology, Chemistry, Communication Disorders, English, History, and Medical Technology. The graduate program was put in jeopardy with the merger of the University of Wisconsin System and the Wisconsin State University System in 1971, and the 33 existing programs at the time would be evaluated by both the university and the UW-System to determine if they were successful enough to deserve further funding. Many existing programs, as well as programs that were slated to start during the 1970s, would be terminated as the university fought hard to keep its graduate program in place, despite a lack of funding and push back from the UW-System. The graduate program as a whole would survive the 1970s, and the 1980s would bring a new dedication to the success of the graduate program. Since the 1980s, there has been a continued importance put on graduate level education at the university. As of 2022, the university offers eleven graduate programs, including several in the nursing, history, and science programs.