The Department of History and Philosophy of Science was established at Indiana University in 1960, largely due to the persistence of Professors Edward Grant and Norwood Russell Hanson. Shortly after Grant came to Indiana University, Hanson approached him with the idea of establishing a program in the History and Philosophy of Science. After garnering the support of other faculty members, a proposal was put forth to the administration, who happily approved the plan. Concerns from the Philosophy Department led to a name change - the Department of History and Logic of Science. The Board of Trustees approved the creation of the new department February 27, 1960.

With four faculty members and nine graduate students, the first year of the Department of History and Logic of Science began the fall of 1960. At the time, the department was primarily a Graduate School program with plans to create a fully-implemented undergraduate curriculum within a few years. The 1960-61 COAS Bulletin states that the intentions of the Department was "to explore, as an independent field of study, the conceptual development of scientific ideas, as well as their integral logical structure." Dr. Hanson served as the first Chair of the department.

A growing department, by the 1963-64 school year, the department had changed its name back to the original Department of History and Philosophy of Science. In the spring of 1964, the department awarded its first degrees - 5 M.A.s, and by the late 1960s, the Ph.Ds the department granted reached record levels, with the peak coming in 1971, with ten Ph.D.s awarded.

From the mid 1970s through the 1980s, class numbers dropped due in part to lack of growth in the field and limited job opportunities. During the 1990s, however, the department experienced a revitalization. The department experienced a substantial revision of its faculty; new hirees brought new perspectives and the department neared its record in the number of Ph.D.'s it granted. In 2000, the department celebrated its 40th anniversary.