Scott County was first inhabited by two bands of the Santee Sioux (Dakota) Indians, the Mdewakanton and Wahpeton. Their semi-nomadic life followed a seasonal cycle. They gathered food, hunted, fished, and planted corn. In the summer the Dakota villages were occupied but in the winter the groups separated for hunting. They had many permanent villages along the Minnesota River. They had many trails leading to these settlements and to the Red River Valley in the North, and the Prairie du Chien to the Southeast. These trails were later used by the fur traders and settlers, and were known as the "ox cart trails." The area of Scott County, as well as much of southern Minnesota, was opened for settlement by two treaties signed at Mendota and Traverse des Sioux, in 1851 and 1853. These treaties removed the Dakota Indians to reservations in upper Minnesota.
Scott County was established and organized by an Act passed in the legislature on March 5, 1853. The 369-square-mile (960 km2) county was named after General Winfield Scott. Settlers started entering the area in the mid-1850s. The Minnesota River and the ox cart trails were the primary transportation routes. The first settlers were Yankees, followed by groups of Germans, Irish, Czechs, and Scandinavians. They each brought their own traditions and religions. Most of these settlers became farmers. Fur trading, lumbering, and farming were Minnesota's major industries all throughout the 19th century. With the fast-growing farms, sprang up towns. Shakopee, the County Seat, began in 1851 as a trading post by the Dakota Village of Chief Shakopee (or Shakpay). Other towns were established alongside transportation routes. When the railroads came to Minnesota they became the primary mode of transportation, and eventually highways were developed along the ox cart trails between the communities.
Due to urban sprawl and suburbanization this rural county is changing dramatically. Cities are continually growing, causing an increase in population from roughly 90,000 in 2000 to 130,000 today, making Scott County Minnesota's fastest-growing county.