[8] It was named in honor of Charles Eugene Flandrau, a judge in the territory and state of Minnesota.

He is credited with saving the community of New Ulm, Minnesota, from destruction during conflict with the Sioux tribe in 1862.

In 2015, the nearby federally recognized Flandreau Indian Reservation of Santee Sioux had planned to open the nation's first recreational marijuana lounge in a former bowling alley, close to its existing Royal River Casino and Hotel.

Any tourists or non-tribal members using marijuana on tribal land risked state prosecution, so they abandoned the plan.

Present-day Flandreau developed near there, with people attracted to the community because of trading business.

[17] The town of Flandreau was originally settled in 1857, and named for U.S. Indian Agent Charles E. Flandrau.

)[18] Like other settlements in the region, it was abandoned within a year, as a result of threatening activities of the Yankton Sioux during the Indian Wars.

In 1869, following the American Civil War, the area was resettled by twenty-five families of Christianized Sioux from the Santee reservation.

Richard F. Pettigrew of Sioux Falls, South Dakota, a relative of Pettigrew settlers in Flandreau, promoted establishing an Indian School at Flandreau as part of what was his successful 1889 campaign in the state legislature to be elected for the U.S. Senate.

The Bureau of Indian Affairs took over a former Presbyterian Church mission school for the facility.