On 1 September 1939, Hitler ordered an invasion of Poland, the opening event of World War II. Poland had signed an Anglo-Polish military alliance as recently as the 25th of August, and had long been in alliance with France. The two Western powers soon declared war on Germany, but they remained largely inactive (the period early in the conflict became known as the Phoney War) and extended no aid to the attacked country. The technically and numerically superior Wehrmacht formations rapidly advanced eastwards and engaged massively in the murder of Polish civilians over the entire occupied territory. On 17 September, a Soviet invasion of Poland began. The Soviet Union quickly occupied most of the areas of eastern Poland that were inhabited by a significant Ukrainian and Belarusian minority. The two invading powers divided up the country as they had agreed in the secret provisions of the Molotov–Ribbentrop Pact. Poland's top government officials and military high command fled the war zone and arrived at the Romanian Bridgehead in mid-September. After the Soviet entry they sought refuge in Romania.

German-occupied Poland was divided from 1939 into two regions: Polish areas annexed by Nazi Germany directly into the German Reich and areas ruled under a so-called General Government of occupation. The Poles formed an underground resistance movement and a Polish government-in-exile that operated first in Paris, then, from July 1940, in London. Polish-Soviet diplomatic relations, broken since September 1939, were resumed in July 1941 under the Sikorski–Mayski agreement, which facilitated the formation of a Polish army (the Anders' Army) in the Soviet Union. In November 1941, Prime Minister Sikorski flew to the Soviet Union to negotiate with Stalin on its role on the Soviet-German front, but the British wanted the Polish soldiers in the Middle East. Stalin agreed, and the army was evacuated there.

The organizations forming the Polish Underground State that functioned in Poland throughout the war were loyal to and formally under the Polish government-in-exile, acting through its Government Delegation for Poland. During World War II, hundreds of thousands of Poles joined the underground Polish Home Army (Armia Krajowa), a part of the Polish Armed Forces of the government-in-exile. About 200,000 Poles fought on the Western Front in the Polish Armed Forces in the West loyal to the government-in-exile, and about 300,000 in the Polish Armed Forces in the East under the Soviet command on the Eastern Front. The pro-Soviet resistance movement in Poland, led by the Polish Workers' Party, was active from 1941. It was opposed by the gradually forming extreme nationalistic National Armed Forces.

Beginning in late 1939, hundreds of thousands of Poles from the Soviet-occupied areas were deported and taken east. Of the upper-ranking military personnel and others deemed uncooperative or potentially harmful by the Soviets, about 22,000 were secretly executed by them at the Katyn massacre. In April 1943, the Soviet Union broke off deteriorating relations with the Polish government-in-exile after the German military announced the discovery of mass graves containing murdered Polish army officers. The Soviets claimed that the Poles committed a hostile act by requesting that the Red Cross investigate these reports.

From 1941, the implementation of the Nazi Final Solution began, and the Holocaust in Poland proceeded with force. Warsaw was the scene of the Warsaw Ghetto Uprising in April–May 1943, triggered by the liquidation of the Warsaw Ghetto by German SS units. The elimination of Jewish ghettos in German-occupied Poland took place in many cities. As the Jewish people were being removed to be exterminated, uprisings were waged against impossible odds by the Jewish Combat Organization and other desperate Jewish insurgents.