The cemetery was established in 1863, by an order from Major General George Henry Thomas after the Civil War Battles of Chattanooga, as a place to inter Union soldiers who fell in combat. 75 acres (300,000 m2) of land was initially appropriated from two local land owners, but later purchased. It became a Chattanooga National Cemetery in 1867. By 1870 more than 12,000 interments had been made, most of whom were unknown. Many nearby battlefield burials were also reinterred in Chattanooga, including nearly 1,500 burials from the Battle of Chickamauga.
During World War I several German prisoners of war who died while in captivity were buried in Chattanooga National Cemetery. After the war, the German government paid to have other POWs disinterred from Hot Springs National Cemetery and moved to Chattanooga.
Chattanooga National Cemetery was listed in the National Register of Historic Places in 1996.
Due to space limitations new burials are expected to be closed by 2015.