Named after General Winfield Scott, who achieved renown during the Mexican–American War, during the middle of the 19th century the fort served as a military base for US Army action in what was the edge of settlement in 1850.

For the next quarter century, it was used as a supply base and to provide security in turbulent areas during the opening of the West to settlement, a period which included Bleeding Kansas and the American Civil War.

It was established to provide protection to the rapidly increasing number of settlers, who were migrating from the Eastern United States.

The post quartermaster, Captain Thomas Swords, was in charge of building Fort Scott's structures, and had to deal with the problems of construction on the Kansas prairie, which had few trees.

Swords found his efforts plagued by lack of wood, skilled labor and working equipment.

By the time it was finished, it was obsolete; three years later, it was abandoned by the military in favor of the more western Fort Riley.

The desertion rate from the fort ranged from 12 to 16%, due to boredom, irregular pay, and hatred for military life.

[4]: 53, 57, 61 [5] Two years after the army abandoned the fort, the buildings were sold by auction to civilians, with two being converted to hotels.

Most of the residents in Fort Scott supported slavery, but those outside the town tended to the free-soil side.

During this time, there were local incidents of murder and attempted arson, typical elements of the guerrilla conflicts that were prevalent in the fighting.

In August 1861, the Union Army took command of Fort Scott, and readied it for the war times.

Fort Scott was one of the few installations that recruited and trained black soldiers for the United States Colored Troops of the Union Army.

Some of the latter feared that the railroad, which had been awarded land for development by the US Government in rights-of-way, would evict them from their squatter homes.

[7]: 5–6  Another feature of the park is 5 acres (2.0 ha) of tallgrass prairie restored as part of an ecology-restoration project.