The area in which Crookston is located was virtually unoccupied during pre-European contact and remained little more than a hunting ground associated with the Pembina settlements until the 1860s. The land in the immediate vicinity of Crookston is not connected with any verifiable Native American or European historic events or circumstances until transfer in the Treaties of Old Crossing in 1863-64. Prior to that time, the territory now included in Crookston was technically a part of Rupert's Land and Assiniboia before becoming part of the United States as a result of the boundary settlement in the Treaty of 1818.

The area in which Crookston is located was traversed by trappers and traders including Ojibwa and Lakota Indians, Métis, and other mixed-race people as well as white men between 1790 and 1870. A branch of the Red River Trails passed nearby; it was used by fur traders between the 1840s and 1870s.