The land for the cemetery was purchased by the town of Baton Rouge from John Christian Buhler Jr, in August 1852, with burials in the area dating back to the 1820s according to some sources.

[3][4] The cemetery was the site of intense fighting during the Battle of Baton Rouge on August 5, 1862;[5] a commemorative ceremony is held at the cemetery each August.

[2] It was turned over to the city of Baton Rouge in 1947 and is now administered by the Recreation and Park Commission for the Parish of East Baton Rouge (BREC).

[3][4] Magnolia Cemetery was added to National Register of Historic Places on January 31, 1985.

These include sugar planter and philanthropist John Hill (1824–1910), novelist Lyle Saxon (1891–1946), and "Florence Nightengale of the South" Confederate nurse Joanna Fox Waddill (1838–1899).