It isn't certain exactly when the Ninnekah Cemetery was originally established or by whom, but the earliest recorded burial occurred in 1904, possibly in the month of May, with the death of infant Bonnie Harmon Irwin, who was born in May of 1904. Mrs. Jeston Coots Gee was also buried in 1904, but her date of death is not known.

On January 10, 1911, the Woodmen of the World, Washita Camp #119, met and voted to officially take over the cemetery, having it surveyed and platted on January 24, 1911. The plat map was duly recorded at the Grady County Courthouse in Chickasha, Oklahoma on January 31, 1911. The cemetery was officially called the W.O.W. Cemetery until the Washita Camp #119 gave up oversight of the cemetery sometime in the late 1960's or early 1970's, at which time it was simply referred to as the Ninnekah Cemetery. Although the Woodmen of the World no longer retained oversight of the cemetery, several of its members continued to care for the cemetery and issue deeds to lot purchasers.

In the summer of 2015, several concerned citizens from the Ninnekah Community formed an informal group called Friends of the Ninnekah Cemetery, and assumed the care of the cemetery. In June of 2023, the group officially began the process of becoming incorporated with the State of Oklahoma, and was approved as such on September 22, 2023, thus becoming a not for profit organization in the State of Oklahoma. The group is now known as The Friends of the Ninnekah Cemetery Association, and is awaiting approval by the Internal Revenue Service to be classified as a 501(c)13, with federal not for profit status.