In 1868 the Yankton Cemetery Association was established to develop a cemetery for the Yankton Territory, The committee consisted of F.J. Dewitt, Bartlett Tripp, Territorial Governor J.L. Pennington, Newton Edmunds, G. Heard, Joseph Ward, E. Wilcox, M. Parmer, J.W. Burdick, J.C. McVay, Jacob Max, L. Wynn, J.R. Sanborn, Peter Seydet, Jacob Bender, G.E. Brooks and W. Miner.

The first recorded burial was James McBinn in 1876. The initial cost for cemetery lots were $12.50 for a lot, $20.00 for half a block and $35.00 for an entire block.

Many prominent figures from Yankton history are buried at the Cemetery, including: General Custer’s bandleader, several Territorial Governors, State Senators and Congressmen and the notorious Jack McCall, who was hung for Wild Bill Hickok murder March 1, 1877.

The Yankton Cemetery Association transferred ownership of the cemetery to the City of Yankton in 1972. The cemetery is non-denominational.