In an effort to direct the growing number of students undertaking graduate studies at Indiana University, a standing Committee on Advanced Degrees was established in1894. All applications went through this committee of six faculty members, and graduate work was under the immediate control of the committee. On May 15, 1902, the committee, then chaired by Professor Carl H. Eigenmann, recommended the establishment of a graduate school, "in order to give dignity and coherence to the graduate work." The school was to be headed by an administrative board consisting of seven department chairs, with the university's vice president serving as ex officio chairman or dean. The administrative board was expected to perform the functions of the current Committee on Advanced Degrees.

Formal organization of the Graduate School was authorized by the faculty in 1904, with the continued governance by the Committee on Advanced Degrees until the office of Dean was created in 1908. This Committee was reorganized as the Administrative Committee of the Graduate School, and in 1909 it became the Graduate Council.

The Graduate Council continued to administer and oversee the school, including issuing recommendations to the Dean who acted on the Council's behalf. Meetings were held upon the call of the Dean to consider questions pertaining to admission requirments, advanced degrees, and various other problems relating to the administration of the school. The Council grew until each department offering graduate courses had a representative sitting at the table. In 1934, the Board of Trustees approved President Bryan's recommendation for recognizing the Graduate School faculty. Prior to this change, faculty members had been listed in some of the catalogs, but were not given official standing and authority as faculty of the School. With this change, the Council was deemed unnecessary and was disbanded.

With the retirement of Dean Fernandus Payne and John W. Ashton's interim appointment as Dean of the Graduate School in 1947, discussions began on the reorganization of the school. Upon the appointment of Stith Thompson as the new Dean, a new organizational structure was established. Within this structure, all faculty teaching graduate level courses would report to their respective school deans, and the school deans would report to a newly formed Graduate Council chaired by the Dean of the Graduate School. The Council also included the Assistant Dean and nine elected faculty, who served a three year term on the Council and were eligible for re-election.

This new Council elected its first members in time for the 1951-1952 academic year. They were charged with reviewing and modernizing the course curriculum, establishing procedures for administration of student programs, and reviewing graduation and admissions requirements.

As of 2007, there are thirty-six active members on the Council.