The Jones Store Company was founded in 1887 by J. Logan Jones with a store opening in Stafford, Kansas. Another store was opened under The Jones Store Company name in Kansas City, Missouri in 1895, and in 1902, Jones leased a 7-story building in Kansas City as well. The store sold a variety of items, including groceries, hardware, stoves, bedding, furniture, fabric for dresses and shoes, and other typical items found in department stores.

In 1910, Jones declared bankruptcy. The company emerged from this under new ownership and was by the 1930s Kansas City's largest department store. In the early 1960s, the Jones Store Company became a part of the Mercantile Stores Company. At this time, the flagship store still remained in business until The Jones Company was acquired by Macy Department Stores in 1998.

The downtown store building was demolished in 2005 with Federated's acquisition of The Jones Store Company. In 2006, The Jones Store Company was assumed by the new Macy’s Midwest division of Federated, and The Jones Store Company name was phased out.