Although the Army post in the area was established in 1875, and construction of Fort Sam Houston began the following year, no burials were made in the area that is currently the cemetery until 1926. In 1931 60 acres (24 ha) were added as an addition to San Antonio National Cemetery. In 1937, the addition became a National Cemetery in its own right, renamed Fort Sam Houston National Cemetery. In 1947 several other forts in Texas, including Fort McIntosh, were closed and their cemetery interments were transferred to Fort Sam Houston National Cemetery.[citation needed]

Interred at the Fort Sam Houston National Cemetery are 140 Axis prisoners of war (POWs) from World War II who died in captivity. 133 are German, 4 are Italian, and 3 are Japanese. These POWs were disinterred from various Texas prisoner of war camps and reburied at Fort Sam Houston National Cemetery.[citation needed] Among these POWs is Hugo Krauss, a German murdered by fellow German POWs at Camp Hearne in 1943.[citation needed] When originally interred, these graves were isolated from the American graves. There are two POW graves that have been erroneously documented as "Nazi" graves because they are marked with the Knight's Cross, a symbol often associated with Nazism. In the context of these POW headstones, the Knight's Cross markings indicate that these two soldiers were awarded the Knight's Cross, one of Germany's highest military awards. These soldiers were probably members of Germany's famed "Afrika Korps", and may have been taken prisoner in North Africa.[citation needed]