The German Army established the military cemetery in Prilep in 1916 for the war dead of the Salonica Front. Between 1931 and 1932 the Volksbund Deutsche Kriegsgräberfürsorge developed the area into a collective cemetery, which was consecrated on 9 May 1933. After the burial of more dead soldiers during the Second World War, the cemetery fell into disrepair and was eventually almost destroyed. The area was used as a pasture for cattle, among other things, and waste was also disposed of there. As there was no war graves agreement, the Volksbund Deutsche Kriegsgräberfürsorge was unable to carry out any maintenance measures for a long time. Talks held in the early 1970s about relocating the cemetery did not result in any concrete measures. Renewed negotiations took place in 2000 and finally, in July 2003, the Volksbund Deutsche Kriegsgräberfürsorge received permission from the Ministry of Labour and Social Policy of North Macedonia to restore the cemetery in Prilep.
1,683 German and 146 war dead from Austria, Bulgaria, Hungary, Romania, Serbia and Turkey as well as eight from Albania are buried in Prilep. During the Second World War, around 50 dead German soldiers found their final resting place here. As part of the restoration of the cemetery from 2003, the cemeteries from the First World War were labelled with groups of symbolic crosses made of granite. The names of all war dead of the First World War known to the Volksbund Deutsche Kriegsgräberfürsorge were engraved in granite stones. In a part of the cemetery that had not been used until then, war dead from the Second World War from Macedonia were buried in individual graves and provided with grave crosses with the names and dates of those buried. Groups of symbolic crosses made of white marble and a name plaque mark the graves of the Bulgarian war dead. A separate memorial plaque commemorates the Hungarian soldiers.
The main path of the cemetery is lined with white and red roses. Benches and lime trees contribute to the design of the cemetery. The original entrance gate to the cemetery was reconstructed using a surviving photo. The Volksbund Deutsche Kriegsgräberfürsorge commissioned a local company to manufacture and install the gate. The work to restore the cemetery was completed in 2014.
Heinrich Ebert, the 19 year old son of Friedrich Ebert (1871-1925), the first President of Germany from 1919 until 1925, was buried in the German Military Cemetery in Prilep. He was drafted into the Reserve-Jäger-Bataillon 11 in August 1916, was seriously wounded in the back and lungs by a shell splinter on 26 January 1917 and died in the military hospital in Prilep on 14 February 1917.