In 1806, Lewis and Clark concluded their two-year trek through the Louisiana territory. When they returned to St. Louis, they spoke with great enthusiasm about one area in particular, where the streams were full of beavers and the plains were rife with buffalo. Inspired by their report, a number of settlers immediately set out to seek their fortune in the newly charted region. Joseph LaFramboise was among the first, building a fur trading post on the western bank of the Missouri River in 1817. In 1831, a representative of the American Fur Company named Pierre Chouteau, Jr. tore down LaFramboise's post and built a new structure which he dubbed Fort Pierre. The U.S. Army purchased Fort Pierre for use as a military post. Even after the army abandoned the site and moved to nearby Fort Randall, a number of people remained in Fort Pierre and it continued to grow.

The Dakota Territory was officially established in 1861. The arrival of the railroad in 1873 and the discovery of gold in the Black Hills in 1874 led to the Great Dakota Boom as settlers began pouring in. The ferry landing established at the railroad terminal across the river from Fort Pierre began to take on a life of its own and, by 1880, had emerged as the new town of Pierre. By the time South Dakota was admitted to the union in 1889, Pierre had already outgrown its neighbor on the other side of the Missouri. When the time came to select a state capital, Pierre campaigned long and hard for the honor against the town of Mitchell, which was further east and closer to South Dakota's population center. The only factor Pierre really had in its favor was its location in the geographic center of the state. This was obviously enough to sway voters; Pierre won the statewide vote by a significant margin and was named the state capital in 1890. The State Capitol, completed in 1910, is still in use today.