Both Aiken County and its county seat of Aiken are named after William Aiken (1779–1831), who was the first president of the South Carolina Railroad Company. Aiken County was organized during the Reconstruction era in 1871 from portions of Barnwell, Edgefield, Lexington, and Orangeburg counties.
Prince Rivers, a freedman and state legislator from Edgefield County, had been a leader in the United States Colored Troops. He was named to head the commission that drew the new county's boundary lines. He was dubbed "The Black Prince" by local newspapers, including the Edgefield Advertiser. He also led the commission that selected the site of Aiken County's present-day courthouse. Other freedmen who were part of the founding of the county were Samuel J. Lee, speaker of the state House and the first black man admitted to the South Carolina Bar; and Charles D. Hayne, a free man of color from one of Charleston's elite families.
Political tensions kept rising in South Carolina during the 1870s, especially around elections. In the months prior to the 1876 elections, Aiken County was one of the areas to suffer white paramilitary Red Shirts attacks and violence directed against black Republicans to suppress the black vote. Between the Hamburg Massacre in July and several days of rioting in September in Ellenton, more than 100 black men were killed by white paramilitary groups in this county. Two white men died in the violence.
In the late 19th century, the county became a popular destination as a winter refuge for affluent Northerners, who built luxury housing. The county remains popular with horse trainers and professional riders because mild winters allow lengthy training seasons.
In the 1950s, Aiken County, along with the nearby counties of Allendale and Barnwell was chosen as the location for storage of nuclear materials and various fissile materials, now known as the Savannah River Site. Ellenton, South Carolina was acquired and its buildings demolished for its development for this plant. Its residents and businesses were all moved north about eight miles to New Ellenton. Developed during Cold War tensions, the facility is now scheduled for decommissioning of various parts of the site.