The Union Methodist Episcopal Church began as an off-shoot of Saint George's Methodist Episcopal Church in the early part of the 19th century and was located on Fourth Street below Arch, in the former Whitefield Chapel.

On March 24, 1825, the Union M. E. church purchased a lot of ground at Ninth and Noble Streets, in the Spring Garden District, for a burying ground. When those streets were subsequently opened, the bodies there had to be removed. In view of the event, the church purchased a lot of ground between Tenth and Eleventh Streets, above Washington Avenue, on January 31, 1832, for use as a cemetery. Later that year, the Machpelah Cemetery Society purchased the lot immediately south of the Union M. E. Cemetery for their own burial purposes.

The Methodist Episcopal Union Cemetery became colloquially known as "Old Union Cemetery" when the Sixth Street Union Cemetery was opened in 1841 by the Union Burial Ground Society.

As far back as 1836, the church had discussed building a new edifice on their cemetery grounds. In 1854 the vision was realized when a church was erected there on the Eleventh Street side and subsequently spun off as a subordinate congregation a few years later.

In 1890, the City Board of Health ordered the closure of the cemetery. When the adjacent Machpelah Cemetery was removed in 1894, it was noted, some bodies of Chinese Methodists who were buried in the Union M. E. Cemetery were removed at the same time and sent back to their families overseas.

By January, 1902, the Board of Health, on request of the Union M. E. Church, granted the congregation permission to remove the 2,500 bodies from the cemetery to Arlington Cemetery in Drexel Hill, Delaware County, so that the cemetery site could be used for building purposes.

Note: due a mapping error, this cemetery is sometimes confused with the Mutual Family Cemetery across Washington Avenue. They are two distinct cemeteries with two distinct histories.