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1939–1945: Experiences during World War II

After Britain declared war on Germany in September 1939, Hepburn's mother moved her daughter back to Arnhem in the hope that, as during the First World War, the Netherlands would remain neutral and be spared a German attack. While there, Hepburn attended the Arnhem Conservatory from 1939 to 1945. She had begun taking ballet lessons during her last years at boarding school, and continued training in Arnhem under the tutelage of Winja Marova, becoming her "star pupil". After the Germans invaded the Netherlands in 1940, Hepburn used the name Edda van Heemstra, because an "English-sounding" name was considered dangerous during the German occupation. Her family was profoundly affected by the occupation, with Hepburn later stating that "had we known that we were going to be occupied for five years, we might have all shot ourselves. We thought it might be over next week… six months… next year… that's how we got through".

In 1942, her uncle, Otto van Limburg Stirum (husband of her mother's older sister, Miesje), was executed in retaliation for an act of sabotage by the resistance movement; while he had not been involved in the act, he was targeted due to his family's prominence in Dutch society. These family events were the turning point in the attitude of Hepburn's mother, who had flirted with Nazism up to this point. Hepburn's half-brother Ian was deported to Berlin to work in a German labour camp, and her other half-brother Alex went into hiding to avoid the same fate.

"We saw young men put against the wall and shot, and they'd close the street and then open it, and you could pass by again... Don't discount anything awful you hear or read about the Nazis. It's worse than you could ever imagine."

—Hepburn on the Nazi occupation of the Netherlands

After her uncle's death, Hepburn, Ella, and Miesje left Arnhem to live with her grandfather, Baron Aarnoud van Heemstra, in nearby Velp. Around that time Hepburn gave silent dance performances that reportedly raised money for the Dutch resistance effort. It was long believed that she participated in the Dutch resistance itself, but in 2016 the Airborne Museum 'Hartenstein' reported that after extensive research it had not found any evidence of such activities. A 2019 book by Robert Matzen provided evidence, based on Hepburn's personal statements, that she had supported the resistance by giving "underground concerts" to raise money, delivering the underground newspaper, and taking messages and food to downed Allied flyers hiding in the woodlands north of Velp. She also volunteered at a hospital that was the center of resistance activities in Velp, and, according to Hepburn, her family temporarily hid a British paratrooper in their home during the Battle of Arnhem. In addition to other traumatic events, she witnessed the transportation of Dutch Jews to concentration camps, later stating that "more than once I was at the station seeing trainloads of Jews being transported, seeing all these faces over the top of the wagon. I remember, very sharply, one little boy standing with his parents on the platform, very pale, very blond, wearing a coat that was much too big for him, and he stepped on the train. I was a child observing a child."

After the Allied landing on D-Day, living conditions grew worse, and Arnhem was subsequently heavily damaged during Operation Market Garden. During the 1944–45 Dutch famine, the Germans hindered or reduced the already limited food and fuel supplies to civilians in retaliation for Dutch railway strikes that were held to disrupt the occupation. Like others, Hepburn's family resorted to making flour out of tulip bulbs to bake cakes and biscuits, a source of starchy carbohydrates; Dutch doctors provided recipes for using tulip bulbs throughout the famine. Suffering from the effects of malnutrition, after the war ended Hepburn became gravely ill with jaundice, anaemia, oedema, and a respiratory infection. In October 1945, a letter from Ella asking for help was received by Micky Burn, a former lover and British Army officer with whom she had corresponded whilst he was a prisoner of war in Colditz Castle. He sent back thousands of cigarettes, which she was able to sell on the black market and thus buy the penicillin which saved Hepburn's life. The Van Heemstra family's financial situation changed significantly through the occupation, during which time many of their properties (including their principal estate in Arnhem) were damaged or destroyed.