The township and city of Fitchburg merged to the City of Fitchburg as a result of Madison's repeated boundary encroachments and efforts to annex portions of the township. This was not an easy process but was eventually settled in favor of Fitchburg by the Wisconsin Supreme Court in 1983. Today the two cities have created neighborly bonds and quite peacefully interact as they share a common history.

Fitchburg itself covers nearly 35 square miles and at one time was part of another township called Rome. Rome also contained part of the present towns of Oregon and Dunn. Then in 1847 Fitchburg separated from Rome and became known as the town of Greenfield which was descriptive of the area's rolling fields and lush greenery. But in 1853, Greenfield renamed itself so as not to create confusion with the town of Greenfield in Milwaukee County.

At the time, the center of government for Fitchburg was in an area known as Oak Hill at the intersection of County M and Fish Hatchery Road. As the center of activity for the area, Oak Hill included an inn called Quiveys Grove (it original location, which also served as the stagecoach stop), a hotel, the regional post office and a building used as the government meeting place. Other settlements were also getting established in the town largely related to stagecoach stops and rail stations. Lake View, Dogtown, Syene, Swan Creek, Stoners Prairie and Fitchburg Village all sprang up and to this day remain as familiar names within the city. Fitchburg Village may have once held the title of "down town" is it featured a railway station, feed mill, creamery, general store, lumber yard and a post office.

Fitchburg was dotted with many one-room school houses and several are still standing while others are marked with historical markers. The city has five sites that are included in the National Register of Historic Places and others that have not yet made the list including the Oscar Mayer Observatory located atop the hill in Fitchburg's Research Park Associates. Built in 1879 and originally located next to Washburn Observatory on the University of Wisconsin campus, it was moved to Fitchburg in 1960.