World War II began in the Pieniny on 1 September 1939. The border was defended by Border Protection Corps outposts that, overwhelmed by larger forces, were forced to withdraw towards Nowy Sącz. The functionaries of the German occupation situated themselves in Szczawnica on 8 September when the Gestapo and the Blue Police each set up a precinct headquarters. The border was controlled by the German Grenzschutz (border guards) with guardhouses in Biała Woda, Szlachtowa and Szczawnica among others.

    One of the main trafficking and courier routes ran through the Pieniny. Transit and liaison points emerged in Szczawnica. Immediately after the September defeat, great numbers of refugees fleeing the now-occupied country started to arrive in the south of Poland. Most of them were civilians but there were also soldiers who wanted to get through to France, where a Polish army was being formed. Traffickers would usually try to smuggle groups numbering from several to a dozen people. After the refugees  crossed the border into Slovakia, guides led them through forests to Košice and then to Budapest. On the return trip, couriers would bring money, secret orders, weapons, and so forth, back to Poland. They also led emissaries, military instructors and other people across the border.

    28 August 1944 saw the outbreak of the Szczawnickie Uprising in Szczawnica and Krościenko, which was a part of the ‘Burza’ (Storm) action of preparations for an uprising in all parts of the occupied country. The commander of the AK (National Army) outpost in Szczawnica, Lieutenant Adam Czartoryski, alias Szpak, attacked the Renata villa that housed 46 Blue Police trainees along with their German instructors.. After the building has been surrounded, the trainees shot their German superiors, yielded to the attackers and swore an oath to Czartoryski. Then they went to the mountains with Szpak’s soldiers to join one of the partisan groups. The Germans brought combat units to Szczawnica and Krościenko to attack the partisans retreating into the Gorce Mountains. Both towns miraculously avoided the harsh pacification measures typical of German reprisals.