Its early history is tied to the establishment of Fort Scott in 1842 to manage relations with Indian tribes in the region, and particularly with the Osage.

[3] The county's first settlers, many of whom were pro-slavery, faced opposition from free-state advocates, leading to violent confrontations during the Bleeding Kansas era and later during the Civil War, such the Battle of Mine Creek in 1864.

[4] The aftermath of the Civil War brought economic and demographic changes; many ex-soldiers settled in the area, contributing to its agricultural growth.

Post-war years saw the railroad's arrival, connecting Bourbon County to broader markets and facilitating the expansion of coal mining and agriculture, particularly wheat, corn, and later, sorghum.

In the spring of 2014 an otherwise healthy man was bitten by a tick, contracting the virus, dying 11 days later from organ failure.

[18] † means a community is designated a Census-Designated Place (CDP) by the United States Census Bureau.

The city of Fort Scott is considered governmentally independent and is excluded from the census figures for the townships.