The post was located on the north side of the Little Osage River and was named for President Abraham Lincoln. The fort consisted of several buildings, including a large blockhouse, surrounded by a five-foot-high earthwork embankment. The town of Fort Lincoln was also established by Lane outside the post in 1861.
Primarily used to house Confederate prisoners, it also served as part of a border defense system of Fort Scott during the Civil War, protecting Kansas residents against attacks from Confederate forces.
After the Battle of Dry Wood Creek, across the border in Vernon County, Missouri, on September 2, 1861, Lane believed that the Confederates would attack Fort Scott the next day. He ordered the town of Fulton evacuated and the citizens and troops to fall back to Fort Lincoln. Soon 1,200 troops, most of the citizens of the town of Fort Scott and some refugees from Missouri, made their way to Fort Lincoln. However, the attack didn’t happen, and the citizens soon returned to their homes.
After the threat to For Scott waned in September 1861, Lane took most of his troops from Fort Lincoln to fight elsewhere but left about 300 infantry and cavalry troops. In 1862, Lane’s force was disbanded, and the post was occupied by black Union soldiers, who guarded the post as a prisoner of war camp. In April 1863, the black troops were replaced by white troops. The post was garrisoned until January 1864, at which time the large blockhouse was moved to Fort Scott.
Fort Lincoln was located about 12 miles north of the city of Fort Scott and just a few miles west of Fulton.