The building that currently houses the Museum of Occupations was opened in 1899. After becoming independent in 1918, Lithuania housed its conscription center here. During the Polish occupation, the building held the Courts of Justice. The Soviets occupied Lithuania in 1940 and began using the building as a prison as they began deportations and killings. The Soviet occupation was interrupted by World War II when the Nazis occupied the country and killed thousands of Jewish people. After the war ended the USSR assumed control and continued their crimes.

Ponary Forest is somewhat of a sister site to the Museum of Occupations. This forest was the location of over 100,000 executions performed by the Nazis. They killed primarily Jews, but also Roma, Soviet prisoners of war, Polish underground fighters, and soldiers of the Lithuanian Territorial Defense Force and buried them in mass graves. In fact, many of the artifacts that can be found in the Nazi occupation room in the museum were recovered from the graves of Ponary Forest.