The outbreak of the Second World War interrupted his fencing career as, immediately after his graduation in 1939, he enlisted in the Polish Navy to fight the Nazis.

Czajkowski then made his way back to the Soviet controlled Lwów and, while waiting to be allowed to cross the Romanian border to rejoin the Polish forces in France, continued his fencing training.

During all his time as a Soviet prisoner, one of Czajkowski's main diversions was to hold a wooden spoon in his hand as though it were a sabre and "practice" fencing - visualizing himself engaged in his favorite activity as a distraction from the hardships of his imprisonment.

After being freed from Vorkuta, Czajkowski spent weeks making his way to Uzbekistan, where he stayed for several months working on cotton and rice plantations.

In 1964 Czajkowski's student, Egon Franke became the first Pole to ever earn an Olympic gold medal in fencing when he won the individual men's foil title.

Czajkowski spent many years as Poland's top coach, creating dozens of national, European, World, and Olympic medalists in all three weapons.