Hillsboro Kansas has two museums, the Mennonite Settlement Museum and the William F. Schaeffler House Museum. Both museums are managed by the City of Hillsboro Museums department, "Hillsboro Museums."

At the Mennonite Settlement Museum visitors experience the history of  pioneer life on the prairies of western Marion County Kansas. Here in the early 1870s immigrant refugee Mennonites came from south Russia and central Poland. Their story is told in the unique 1876 Peter Paul Loewen House and the replica 1876 Jacob Friesen flouring windmill.

Later the town of Hillsboro was built as a railroad center for shipping wheat to market. The city grew and prospered. A leading family business in Hillsboro was the Schaeffler Mercantile Store. In 1909 prosperous William F. Schaeffler built a beautiful Queen Anne house, now the William F. Schaeffler House Museum. Tours of both museums start at the Hillsboro Museums Visitor Center located west of the Mennonite Settlement Museum on Memorial Drive in Hillsboro.