World War II in Yugoslav Macedonia started with the Axis invasion of Yugoslavia in April 1941. Under the pressure of the Yugoslav Partisan movement, part of the Macedonian communists began in October 1941 a political and military campaign to resist the occupation of Vardar Macedonia. Officially, the area was called then Vardar Banovina, because the very name Macedonia was prohibited in the Kingdom of Yugoslavia. It was occupied mostly by Bulgarian, but also by German, Italian, and Albanian forces.

Initially there was no organised resistance because the majority of the Macedonian Slavs were pro-Bulgarian oriented. It started to grow only in 1943 with the capitulation of Italy and the Soviet victories over Nazi Germany. The role of the Bulgarian communists, who avoided organizing mass armed resistance, was also a key factor. Their influence over the Macedonian Party organization remained dominant until 1943, when it became obvious that Germany and Bulgaria would be defeated.

At that time Tito's special emissary Svetozar Vukmanović arrived in Macedonia. Vukmanović had to activate the struggle and give it a new ethnic Macedonian facade. This led to the rise of younger generation anti-Bulgarian oriented partisan leaders, who were loyal to Yugoslavia. They formed in 1943 the People's Liberation Army of Macedonia and the Macedonian Communist Party. In the western part of the area, the Albanian Partisans also participated in the resistance movement.

After Bulgaria switched sides in the war in September 1944, the Bulgarian 5th. Army stationed in Macedonia, moved back to the old borders of Bulgaria. In the early October the newly formed Bulgarian People's Army together with the Red Army reentered occupied Yugoslavia to blocking the German forces withdrawing from Greece. Yugoslav Macedonia was liberated in end of November when communist Yugoslavia was established. After the German retreat forced by the Bulgarian offensive, the conscription of Macedonians in the army increased significantly.

The operation was called the National Liberation War of Macedonia (Macedonian: Народноослободителна борба на Македонија, Narodnoosloboditelna borba na Makedonija) by the Yugoslav Marxist historiography, in line with the greater Yugoslav People's Liberation War. Some of the combatants also developed aspirations for independence of the region of Macedonia, but were suppressed at the end of the war by the communist authorities. It marked the defeat of Bulgarian nationalism and the victory of the pro-Yugoslav Macedonism in the area. As result the new Communist authorities persecuted the former collaborationists with the charges of "Great Bulgarian chauvinism" and broke up all the organisations that opposed the Yugoslav idea and insisted on Macedonian independence.