The City of Humboldt was founded in 1857. The name Humboldt came from Baron von Humboldt. During the winter of 1856-1857 colonization of Humboldt began by German immigrants migrating from Hartford, Connecticut. Shortly thereafter a sawmill, gristmill, and church were built.
On September 1, 1861 Humboldt was attacked by a group of Osage Indians and border ruffians. The group, led by John Allan Matthews of Oswego, took several recently freed African-Americans back into captivity. This led to a union of the Humboldt Home Guard and the Kansas 6th Cavalry to launch a counter attack. On September 18, 1861, Matthews was killed at Chetopa.
In 1866 Humboldt was organized as a village. By 1870 Humboldt was incorporated and was home to a rail line of the Leavenworth, Lawrence, and Galveston railway. From 1858 to 1865 Humboldt served as the county seat of Allen County until losing an election which resulted in the county seat being moved to Iola.
Humboldt was very involved in the Civil War. After the attack by the Osage Indians and border ruffians, Humboldt formed two home guard companies. On October 14, 1861, Humboldt was again attacked. Humboldt was mostly destroyed by fire.
In 1888 gas was discovered only a few hundred feet east of the Neosho River. Within 10 years, gas was being piped to homes and businesses within Humboldt. This led to job growth. The Humboldt Brick Manufacturing Company was founded in 1897. The brick company produced enough brick to build a school building in 1898. Oil production soon followed the discovery of gas. In 1904 Standard Oil came to Humboldt. Standard Oil decided to build a pipeline to serve refineries at Kansas City and Whiting, Indiana. In 1906 the brick plant doubled in size, and by 1907 Humboldt celebrated the establishment of the Humboldt Portland Cement Company (Monarch). Monarch has remained one of the main employers of residents in the area.
In 1987 B&W Trailer Custom Truck Beds was founded in Humboldt by Roger Baker and Joe Works. Together they revolutionized the gooseneck hitch industry. Since 1987 B&W Custom Truck Beds has seen amazing growth, and continues to be a large source of employment for Allen and surrounding counties.