Given the current challenges and threats to national security, including armed conflicts near the borders of Ukraine, the study of the historical experience of the organization, regulation and activities of the military justice system with the onset of the special period of wartime became actual. Within the specified context study of these issues in a rather difficult period of transition from peacetime to wartime in Ukrainian territory on the beginning of the Great Patriotic War and the occupation of the territory of the USSR by troops of Nazi Germany (1941–1942) is noteworthy. At the same time, the specified experience can be useful during the reformation period the law enforcement system of Ukraine. Results. The article outlines the main objectives and directions of activity of the military justice system in a special period of martial law in the territory of Ukraine. Conclusion. Since the beginning of the war the military courts were entitled to consider not only the cases involving crimes of military, but also civilians and prisoners of war and foreigners. In legal documents, that somehow regulated the activities of military justice system, demands were made for conducting a ruthless struggle against disorganizers of the rear, deserters, panic-mongers, disseminators of rumors, the elimination of spies, saboteurs and enemy parachutists, neutralizing of dangerous individuals, the implementation of strict control of suspicious groups of citizens and maintenance of revolutionary order and discipline. In addition, almost all decision-making decrees required to use fast and balanced approach to the establishment of penalties for offenses, while strictly adhere to the provisions of existing laws and guidance documents.