During the Civil War, the mill was operated by Samuel Hockman. Following the Battle of Fisher Hill, Union General Sheridan began his infamous march. The legend goes that Hockman, upon seeing the other mills burning, rushed to set a Union flag over the mill before running out to meet them. Between that and Hockman's fast talking, Sheridan's men, lead by Brigadier General Custer, were convinced to leave the mill alone.
After the war, Zirkle Mill continued operating well past the turn of the century. However, it could not keep up with modern factories and was forced to close down in the late 1940s. Today, the mill is owned by two descendants of Andrew Zirkle that intend to restore the property for future educational purposes. The mill was added to the National Register of Historic Places in 1983.