In the early 1850s, the towns of Westport and Kansas found themselves in a quandary. The cholera epidemic of 1849 filled the cemeteries of both communities. With expanding boundaries and increasing populations, city leaders started looking for more burial space. In 1857, their search ended when James M. Hunter deeded 49 acres to the Union Cemetery Association. The corporation was organized by a special act of the Missouri General Assembly on November 9, 1857. The new cemetery was located between Westport and the town of Kansas and was to be used by both towns, becoming a "union" between the two. That is how Union Cemetery got its name.

When Union Cemetery was dedicated, it was thought that the 49 acres would accommodate all the deceased in Westport and Kansas City for all time. Little did city leaders suspect that Westport and Kansas City would become one community and that Union Cemetery would lie in the midst of a busy metropolitan area.

By 1910, Union Cemetery was showing increasing signs of deterioration. To raise funds for maintenance, the Cemetery Assocation sold 18 acres at 27th and Main streets. It was later discovered that several members of the association had formed the Evergreen Land Company and had sold the land to themselves, which they later squandered in several land deals. The cemetery association deeded the remaining 27 acres to Kansas City in 1937. The Parks and Recreation department now maintains the grounds.

In August 1889, cemetery records were lost when the secton's cottage caught fire. This was a major loss because many of the graves were identified by wooden or limestone markers that were destroyed by weather, leaving hundreds of unmarked and undocumented graves. The sexton's cottage was burned again and on Halloween night 1985. This time, the cemetery records were kept off site, so none were destroyed. The cottage was rebuilt by the Women in Construction of Kansas City and rededicated in October 1990.