The central part of the structure on this site was dedicated in September 1856. The building was designed in an Eclectic style—one inspired by the New England Colonial style with classical elements—attributed to Elijah Shumway Town and constructed of locally quarried limestone.

A violent storm in 1877 knocked down the original steeple, which was replaced in 1974—now the tallest steeple in Kane County. The Christian Education wing was added to the north of the original church in 1966 and Paxton Hall, a large multipurpose space to the south, was completed in 2005.

The church was established in August 1835 as “The Church of the Big and Little Woods” at the cabin of Thompson Paxton, southeast of Batavia, and affiliated with the Presbyterian church as the first organized religious denomination in Kane County.

The congregation relocated to Batavia Avenue in January 1841. The large number of non-member donors prompted the congregation to create a Congregational Society, which included all subscribers regardless of denomination, and to share the building with the community. In late 1843, the membership affirmed its anti-slavery doctrine by creating the “Congregational Church and Society of Batavia.”