On 23rd August, 1939, just prior to its attack upon Poland, Germany signed a secret agreement with the Soviet Union, on the division of the spheres of influence, the document known as the secret Hitler-Stalin Pact (Ribbentrop-Molotov Pact). Initially, Lithuania was relegated to the German sphere of influence; however, on Lithuania's refusal to attack Poland as a German ally, it was transferred to the Soviet sphere of influence, in a second secret pact signed in Moscow on the 27th of September that same year.

On the 10th of October 1939, Vilnius was returned to Lithuania and Soviet military bases were established within the country.

On the 15th of June 1940 (the day when the German Wehrmacht entered Paris), the Soviet Union occupied Lithuania. Soon afterwards, Latvia and Estonia were also occupied.

On the 14th of June 1941, the Soviets carried out the first mass deportation of the Lithuanian people to Russia and Siberia, with approximately 35,000 deported within several days.

On 22nd June 1941, Germany attacked the Soviet Union and several days later, the Wehrmacht occupied the whole of Lithuania.

Until the Germans had fully consolidated their position, Lithuanian politicians and representatives of the intelligentsia organised an independent government for the country. However, the new occupation force's administration did not allow the existence of a Lithuanian government. A massive destruction of the Jews was launched, claiming 200,000 lives. Thousands were taken to Germany.

In the summer of 1944, the Red Army crossed the Lithuanian border once again, and occupied Vilnius, occupying Klaipeda in January 1945. Once again, the entire country fell under Soviet power. In accordance with the Yalta and Potsdam Agreements between the Soviet Union, the United States of America and Great Britain, Lithuania began to be treated as a part of the Soviet Union. Thousands of Lithuanians, who had fought as soldiers of the armies of the anti-Hitlerite coalition, could not return to a free homeland.