During the Nazi occupation, Karel Štipl was involved in the resistance movement and collaborated with the Sokol resistance organization. He helped families persecuted by the Nazis. The Gestapo arrested him and his wife on December 15, 1944. He was initially held in the Pankrác Prison and then transferred to the Police Prison in the Small Fortress Terezín in February 1945. Even though he fell sick in the Fortress, he continued to paint, debate with fellow inmates, and lecture on his branch in the cell, displaying great strength in the face of aggravated conditions. Using improvised sculpting tools, he made several models, sculpted out of clay brought from nearby brickworks. Their postwar casts (PT 5897, PT 5898) are today kept in the historical art subsection of the Terezín Memorial collection. Karel Štipl was imprisoned in the Small Fortress until its liberation. He returned home to Prague on May 10, 1945.

After the war, he resumed his sculpting, architectural, and art glassware projects as well as his teaching career. He participated in completing many major private and public orders. In 1959, he received the Order of Labor for his distinguished working results. Karel Štipl died on August 22, 1972, at the age of 83, and is buried in the Šárka cemetery in Prague´s Dejvice district.