Jedediah Hotchkiss died at his home in Staunton at age 71. He is buried there in Thornrose Cemetery. The small town of Hotchkiss, West Virginia, in Raleigh County was named for him. The magnificent Queen Anne- and Eastlake-style mansion Hotchkiss built in 1888 at 437 East Beverley Street, Staunton, Virginia, still stands. It is listed on the National Register of Historic Places and Virginia Landmark Register as The Oaks. It is currently in private ownership after a sale in February 2019 by the family that purchased it from the Hotchkiss heirs in 1948.