Boerne came into being as an offshoot of the Texas Hill Country Free Thinker Latin Settlements, resulting from the Revolutions of 1848 in the German states. Those who came were Forty-Eighters, intellectual liberal abolitionists who enjoyed conversing in Latin and who believed in utopian ideals that guaranteed basic human rights to all. They reveled in passionate conversations about science, philosophy, literature, and music. The Free Thinkers first settled Castell, Bettina, Leningen, and Schoenburg in Llano County. These experimental communities were supported by the Adelsverein for one year. The communities eventually failed due to lack of finances after the Adelsverein funding expired, and conflicts of structure and authorities. Many of the pioneers from these communities moved to Sisterdale, Boerne, and Comfort.
In 1849, a group of Free Thinker German colonists from Bettina camped on the north side of Cibolo Creek, about a mile west of the site of present Boerne. They named their new community after Cicero's Tusculum home in ancient Rome. In 1852, John James and Gustav Theissen, who helped settle Sisterdale, platted the townsite, renamed it in honor of German author Karl Ludwig Börne, with the Anglicized spelling of "Boerne". The town was not incorporated until 1909. August Staffell was the original postmaster in 1856.
During the Civil War, Boerne voted against secession and was a mostly pro-Union town; many communities in Kendall County were part of the formation of the Union League, which supported the Union and Abraham Lincoln.
The 1870 limestone courthouse, second-oldest in Texas, was designed by architects Philip Zoeller and J. F. Stendebach, and stands directly across the street from the current 1998 courthouse designed by architects Rehler, Vaughn & Koone, Inc.