Almost a decade before Nebraska became a state, the federal government established a reservation for the Omaha Indian tribe in what today is Thurston County, as well as small portions of Dixon, Burt and Cuming Counties. Eventually the northern half of the reservation was purchased from the Omahas for use as a reservation for the Winnebago tribe.

The county's boundaries were established in 1855 by the Territorial Legislature. For a time the area was referred to as Blackbird County, in honor of Omaha Indian Chief Blackbird. When legislators attempted to formally name the county Blackbird in 1887, Gov. John Thayer vetoed the proposal. Two years later the Legislature adopted an act establishing the county's present boundaries and officially naming it after U.S. Sen. John M. Thurston of Nebraska.

There is an interesting footnote regarding Chief Blackbird. One of his favorite campsites was located on a hill overlooking the Missouri River. According to Indian legend, when Chief Blackbird died his followers seated him on his horse and buried him at this site.

Federal government officials opened a portion of the Omaha Reservation to white settlers in 1884. The following year the area's first village was established. Buildings from the hamlet of Athens were moved to what is now Pender, the county seat, about two miles to the northwest.

With the passage of the railroads through Thurston County in the early 1900s, additional communities began to be established. One of those communities is Emerson, located in the far northwest corner of the county. Emerson is unique in that it is actually Nebraska's only tri-county community, with sections actually platted in Thurston, Dixon and Dakota counties. Visitors who attempt to locate the exact spot where than can stand and be in all three counties have a difficult time, however, since it is located on Main Street, which is also a state highway.