On September 1, 1939, the armed forces of Nazi Germany invaded Poland from the west initiating World War II. Two weeks later, on September 17, Soviet Union joined Germany in their attack on the Second Polish Republic. By early October, Poland was defeated. The occupied Poland was the only country in Europe where the Nazis had introduced a total ban on regional sports clubs. Football was allowed to be practised only by the Germans in the annexed areas of Upper Silesia. Polish activists and players risked their lives by organizing clandestine football competitions in Kraków, Warsaw and Poznań.

Following Molotov–Ribbentrop Pact, Poland was split between the two occupiers. Eastern regions were annexed by Soviet Union's republics of Ukraine and Belarus, while western part was either directly annexed into Germany, or became General Government – a separate region of the Greater German Reich. The region of Wilno was annexed by Lithuania. Because of the war, ongoing games of the 1939 season of Ekstraklasa were cancelled (if not outright abandoned), with Ruch Chorzów being the top team (see 1939 Ekstraklasa). Furthermore, friendly games of Poland national football team with Yugoslavia and Romania, planned for September 1939, were also cancelled.

Football in Soviet-occupied Poland (1939 - 1941) In 1939, only one of Ekstraklasa's ten teams was from the region which was later annexed by the Soviets. It was Pogoń Lwów, but in the city of Lwów itself (which is the birthplace of Polish football), there was a number of other teams, such as Czarni Lwów, Lechia Lwów, Hasmonea Lwów, and Ukraina Lwów. Other well-known teams from Soviet-occupied Eastern Poland were Junak Drohobycz, Rewera Stanisławów, Kresy Tarnopol, Ognisko Pińsk, Strzelec Janowa Dolina and WKS Grodno. Little is known about the fate of teams and players from other locations of Soviet occupied Poland, except from the city of Lwów itself.

Unlike German occupiers in Western Poland, the Soviets allowed selected Poles to play football. At the same time, however, all Polish teams were closed, and replaced with Soviet ones, which used the facilities of former Polish teams. Legendary coach Kazimierz Górski, who spent his youth in Lwów and before 1939 had played for RKS Lwów, in the years 1940 - 1941 and 1944, put on the jersey of Soviet teams Spartak Lvov and Dynamo Lvov, before moving to Warsaw in 1945. Other famous players from Lwów, who were allowed to compete in Soviet-sponsored teams, were popular goalkeeper Spirydion Albański and Wacław Kuchar, who was coach of Dynamo Lvov (1939–1941, 1944–1945). Furthermore, Michał Matyas (top scorer of 1935 Ekstraklasa), played for Dynamo Kyiv, and Adam Wolanin, after one year at Dynamo Lvov, moved to play shortly for Spartak Moscow, together with Bolesław Habowski, who played both for Dynamo Moscow and Spartak Moscow. Jan Wasiewicz ended up in Polish Armed Forces in the West, and Adolf Zimmer Pogoń Lwów was murdered in the Katyń Massacre. Wacław Jerzewski, who was Pogoń's player and coach in 1938 - 1939, was after September 1939 interned in Romania, then fought in general Władysław Anders Corps, and returned to Poland after the war.

Little is known about wartime matches of Polish teams from Eastern Poland. Bohdan Tuszyński in his book Za cenę życia (For the price of life) wrote that on July 2, 1944, in German-occupied Lwów, a game between Polish team of the city and German team KONA took place. The Poles won 4–2.

Currently, the memory of the teams from Lwów (now: Lviv, Ukraine) is still vivid in Poland. Among teams which are regarded as successors of Pogoń, there are Polonia Bytom, Odra Opole, and Pogoń Szczecin, while Lechia Gdańsk, with its white-green hues, is a successor to Lechia Lwów. Also, in autumn of 1946 in Lwówek Śląski, sports club Czarni Lwówek was founded, which owes its name to Czarni Lwów. There were several other teams named Czarni in former German province Lower Silesia, where inhabitants of former southeastern Poland moved after the war - Czarni Jelcz-Laskowice, Czarni Żagań and Czarni Otmuchów.

Very interesting is the story of players and officials of Junak Drohobycz, who became actively involved in Polish resistance movement. Before the war, Junak was a team sponsored by the Polish Army, and in late 1939, members of the club created the White Couriers - a boyscouting organization, which smuggled hundreds of persons from the area of Lwow to Hungary, across the newly created Soviet-Hungarian border in the Carpathians. One of the couriers was Stanisław Gerula, goalkeeper of Junak. Most of players of Junak, who at the same time were soldiers, left Drohobycz in the night of September 11/12, 1939. A few days later they reached Hungary, where Colonel Mieczysław Mlotek, manager of Junak, decided to recreate the team. Junak played several games both in Hungary, and Yugoslavia, among top players there were Antoni Komendo-Borowski (previously of Jagiellonia Białystok and Pogoń Lwów) and Henryk Kidacki. In the second half of 1940, all players together with management moved to Tel Aviv, where several games were organized. In 1942, Junak, known as The Team of Polish Army in the East, was in Iraq. Among others, it beat Iraq 6-1 (January 29, 1943), and Iran 3-1 (March 12, 1942, with General Władysław Anders watching the game). The Poles also faced the team of the British Army (with Harry Goslin, Stan Hanson, Don Howe and Ernie Forrest). The game took place in Baghdad.

In late stages of the war, Junak, together with the army, moved to Italy. In 1944 in Naples, the Polish team, under the new name The Carpathians faced the team of Naples, with 35000 in attendance. Besides players from former clubs from Eastern Poland, the Carpathians also capped stars of Polish football from Upper Silesia, who had been drafted into the Wehrmacht, and were caught by the Allies or deserted in Western Europe - Edmund Giemsa, Ewald Cebula, Henryk Janduda of AKS Chorzów, Zygmunt Kulawik of Śląsk Świętochłowice.,

In mid-October 1939, a little-known game took place in Starosielce in the suburbs of Białystok. Soviet troops, which had entered the area a few weeks before, decided that there would be a football match between Polish team of Starosielce and a Red Army team from a unit stationed in nearby Choroszcz. After first half, despite several brutal fauls of Soviet players and partisan refereeing, the Poles were winning 2–0. During the break, an NKVD officer approached the manager of the Poles, telling him that Poles had to lose. Thus, the match ended in a 3–2 Soviet win.Musicie przegraç ten mecz

Football in Lithuanian-occupied city of Wilno (Vilnius) (1939 - 1940) The city of Wilno was home to several teams, but only one, Śmigły Wilno played one season in the Ekstraklasa (see: 1938 Ekstraklasa). On September 19, 1939, Wilno was captured by the Soviets, who on October 26 handed it over to Lithuania. The Soviets returned in June 1940. Little is known about history of Polish football in Wilno during the war. The Lithuanians created their own teams, and players of Śmigły joined them. Defender Bolesław Zawieja played for LFLS Vilnius, forward Józef Tumasz for LGSF Vilnius, goalkeeper Ludwik Łoś and defender Konstanty Paszkiewicz for JSO Vilnius. On June 16, 1940, as Gazeta Codzienna Polish language daily announced, a match between teams of Kaunas and Vilnius took place. Vilnius’ team was almost exclusively made of Polish players of pre-1939 Śmigły, and Kaunas won 6–1. Longin Korwin-Pawłowski, the only player of Śmigły who capped for Poland in 1937, ended up in a German POW camp, and after the war settled in Canada, where in 1968 - 1969 he was leader of Polish scouting.

Football in German-occupied Poland (1939 - 1945) Following Polish September Campaign, the Germans occupied western and central Poland, the area where football was much better developed. Out of ten teams of the 1939 Ekstraklasa, only one came from Eastern Poland (Pogoń Lwów), and main centers of interbellum Polish football were located in Warsaw, Kraków, Poznań, Łódź, and Polish part of Upper Silesia. German occupiers immediately banned all ethnic Poles from playing football, allowing only those who signed the Volksliste. As a result, all Polish clubs were closed, except for those from Upper Silesia, which were allowed to operate under new, German-sounding names.

Football in German-occupied Warsaw In 1939, Warsaw had two teams in Ekstraklasa - Polonia Warszawa, and Warszawianka Warszawa. Immediately after capture of the city, the Germans closed all Polish clubs, and players were forced to go underground. In spring of 1940, first games were organized in Mokotów Field by Józef Ciszewski, former player of Cracovia and Legia Warsaw. Soon afterwards, in summer of 1940, regular games started, with prewar teams participating under changed names - e.g., players of Polonia Warszawa created teams of Pochodnia, Czarni, and Bimber. Before German authorities seized Polonia's stadium on Konwiktorska Street, in September 1940, a tournament with thirteen teams took place there. In the final game (September 13, 1940), Czarni beat Bimber 3-1.

On December 24, 1941, Alfred Nowakowski created underground Warsaw District of Association Football, and in 1942 games of Warsaw Championship began, with teams not only from Warsaw, but from suburbs, such as Wołomin, Góra Kalwaria, Brwinów, and Piaseczno. Both in 1942 and 1943 champions were re-created Polonia Warszawa. Since matches attracted thousands of fans, and Warsaw was too dangerous because of presence of numerous German soldiers, most of them took place in the suburbs, in such towns, as Piaseczno, Konstancin-Jeziorna, Błonie, and Mirków. In Piaseczno, on Easter Boxing Day 1943, a game between the teams of Warsaw and Kraków took place, ending in a 1–1 draw, with hundreds of spectators watching. Also, in mid-1942, an unusual game took place in Legionowo. Huragan Wołomin faced a team made of German and Bulgarian soldiers, stationed in the town. Poles won 3–2, after a very heated match. Among most active football teams of occupied Warsaw was Okęcie Warszawa, which played over 100 matches. During the war, Okęcie kept four teams, including two of junior players. In 1942, Okęcie was second in Championship of Warsaw, after Polonia.

Last wartime championship took place in 1944, but due to Warsaw Uprising, it was not finished. With some fifty teams, Warsaw was one of main centers of Polish football in those years, which was confirmed in the first postwar Polish Championship (1946), won by Polonia.

Football in German-occupied Kraków Kraków was another center of Polish football - in 1939 Ekstraklasa, out of ten teams, as many as three (Wisła Kraków, Cracovia Kraków, and Garbarnia Kraków) were from that city. It took only a few weeks of occupation for local football officials and players to organize first underground wartime game. On October 22, 1939, in Bronowice, Wisła beat Krowodrza 3-1.

On August 7, 1940, first wartime Championship of Kraków began in Sports Park Juvenia. A few days earlier, on July 23, Hans Frank had issued a decree, which officially dissolved Polish associations, including sports clubs on the territory of General Government. However, Juvenia official Aleksander Wódka was allowed to use the grounds of the Sports Park in any way he liked, so football pitch there for two years was the arena of a number of matches, with German authorities giving unofficial permission. Eight teams participated in the 1940 Championship: Bloki, Cracovia, Garbarnia, Groble, Juvenia, Sparta, Wisła and Zwierzyniecki, and the champion was Wisła, winning all games, with goal difference 52-8. Second was Cracovia, third Garbarnia. The tournament was popular among local fans, attracting up to 3000 people for top games.