Seymour Wilcox was the first man to select the area now known as Waupun as the location for his home.In 1840, the Postal Service was inaugurated in Waupun, and at that time the name of the settlement was to be "Waubun," which translates to "dawn of day." However, an error resulted in the spelling of the settlement as "Waupun," and the name remained. Waupun was officially incorporated as a city in the year 1878.

The End of the Trail is a significant symbol because James Earle Fraser's world-famous equestrian statue stands in Shaler Park in Waupun. Clarence Shaler, a successful Waupun manufacturer, commissioned the bronze casting of the statue and gave it as a gift to the City of Waupun.

The Waupun Library Association survived until 1904 when the City of Waupun established the Waupun Public Library, making the Waupun Public Library one of only three public libraries in the state of Wisconsin that can trace a continuous line back to the city's library association (the other two libraries in this category are the Milwaukee and Madison public libraries). It was in that year that construction began on the Waupun Public Library building shown in the picture at the left.

Library service continued in this building until 1968, when construction was completed and opening ceremonies conducted on the current library building. In 1998, an addition to the current building was completed to increase the amount of space for the growing collection.