According to the Umpqua Heritage Program of the US Forest Service, Yoncalla  is of “uncertain origin, it meant “home of the eagles” and was the name of a butte near present-day Yoncalla that was an eagle nesting area. The Yoncalla Indians, a Kalapooian tribe, were apparently named for this butte. The Yoncalla High School teams are appropriately named “The Yoncalla Eagles.”

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The town was named by its most famous postmaster, Jesse Applegate. The three Applegate brothers were personal friends of Abraham Lincoln from their days in school together. (Source: Pioneer History, Douglas County.)