Batavian John Gustafson and his brothers and sisters were first to see the vision of a viable Batavia Historical Society when they began gathering and cataloging Batavia artifacts in 1959. By 1960, the Batavia Historical Society was established and its mission remains to collect, preserve, study, interpret, and exhibit materials in the Depot Museum.

In 1969, twenty local businessmen donated $50 each to purchase the abandoned C.B. & Q. passenger depot on South Van Buren Street to house historical society collections. In 1973, the Depot was moved from Van Buren Street to its present home on Houston Street. The C.B. & Q. caboose was moved to the Museum campus two years later.

By the time the Depot Museum was dedicated in 1975, almost half the people in town had contributed to the project through their dollars, artifacts, skills or other talents. By 1979, the Depot Museum was listed on the National Register of Historic Places.

The Museum is a cooperative effort between the Batavia Park District and the Batavia Historical Society. Volunteers donate more than 1800 hours each year and the Museum has over 4000 visitors every year including residents, students, and visitors.

As the community has grown, the collection of historical materials has grown and the needs of the community have evolved. The Gustafson Research Center opened in 2000. It is aptly named in honor of John Gustafson and his family who helped establish the Batavia Historical Society. The Center was added to the Museum to provide a dedicated space for the large collection of historical documents and to make these documents accessible to researchers.

The Depot Museum is ideally located close to cultural and civic landmarks, galleries, and outdoor activities.