The mill was built in 1888–1889 by William E. Thomas, a local entrepreneur who owned a flour and feed business in Fergus Falls.

During that time, wheat was a high-demand crop, and nearly one thousand flour mills were in operation throughout Minnesota.

It was very successful during its initial several years of operation, and in 1895 Thomas built an addition to grind buckwheat and rye.

A local resident and activist, Geneva Tweten, led a campaign to save the mill as a symbol of the rural life.

Otter Tail County purchased the site in 1965, and it was listed on the National Register of Historic Places in 1975.