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Choctaw County was originally part of the Choctaw Nation, with Choctaw settlements known to be in the vicinity of Pushmataha prior to the removal of Native Americans from the southeastern United States during the Trail of Tears.
Most of the early European American pioneers of Choctaw County were farmers from North and South Carolina. In 1912 the Alabama, Tennessee and Northern Railroad was completed through the county from north to south, connecting the area to the Port of Mobile and northern Alabama. It induced a population shift from areas near the Tombigbee River to the central part of the county.
The county's population reached its peak in the 1920s, due in part from jobs created by a sawmill boom with companies as the E. E. Jackson Lumber Company and Choctaw Lumber Company. The sawmill industry collapsed during the Great Depression. The first successful oil well in Alabama was drilled at Gilbertown in 1944, with oil and gas becoming the county's most important industry. This industry waned by the 1970s as the wells lost profitability.
An African-American family, the Thorntons of Mobile, was featured in the September 24, 1956, issue of Life Magazine. The article included an interview with the Thorntons' daughter, Allie Lee Causey, of Shady Grove in Choctaw County. In the article, Mrs. Causey, a schoolteacher, spoke openly about her family's life, stating that "integration is the only way in which Negroes will receive justice. We cannot get it as a separate people. If we can get justice on our jobs, and equal pay, then we'll be able to afford better homes and good education." When the magazine was seen in Choctaw County, the Causeys were subjected to brutal economic retaliation by white residents, who tried to coerce Mrs. Causey into recanting her remarks. Their loans were called in, local stores refused to sell them food and gasoline, Willie Causey was cut off from his employment as a woodcutter, and Mrs. Causey was fired from her job as a teacher. The Causeys left Shady Grove and Alabama for good in October 1956.
Apparel factories opened during the 1950s–60s in Silas, Toxey, and Butler, although the plants had largely closed by the 21st century. The 1950s also saw the building a paper mill at Naheola, now owned and operated by Georgia-Pacific. The county was declared a disaster area in September 1979, due to damage from Hurricane Frederic. The 1980s saw the main railroad close and the tracks removed.