In December of 1941 Borrel's resistance group was uncovered and she fled to Lisbon, Portugal. There, she worked at the Free French Propaganda Office for a short time until April of 1942 when she traveled to London, England. From General de Gaulle's Free French bureau she learned about the French Section of the Special Operations Executive and immediately signed up.
On the night of September 24, 1942, Andrée Borrel and fellow SOE agent, Lise de Baissac (Odile) became the first female agents to be parachuted into occupied France. In the darkness, Baissac dropped near Poitiers while Borrell dropped into a field near the village of Mer, not far from the Loire River and was picked up by members of a local resistance team. Because of her intimate knowledge of Paris, Andrée Borrel was sent there to work as a courier for the new "Prosper" network run by Francis Suttill. Her boss was impressed with Borrel's performance and in the Spring of 1943 she was made second in command of the Paris network.
Probably because of a traitor, in June of 1943 several members of the "Prosper" network were arrested by the Gestapo, including network leader Francis Suttill and Andrée Borrel. She was interrogated in the Gestapo's Parisian headquarters and then held in Fresnes prison. She remained there until May of 1944 when, together with three other captured female SOE agents, Vera Leigh, Sonya Olschanezky and Diana Rowden, Andrée Borrel was shipped to the Natzweiler-Struthof concentration Camp camp in the Vosges Mountains of Alsace.
Posthumously, the government of France awarded her the Croix de Guerre in recognition of her heroic sacrifice for her country's freedom. The concentration camp where she died is a now a French government historical site and a plaque to Andrée Borrel and the three women who died with her is part of the Deportation Memorial on the site. As one of the SOE agents who died for the liberation of her country, Lieutenant Borrel is listed on the "Roll of Honor" on the Valençay SOE Memorial in the town of Valençay, in the Indre département of France.
In 1985, SOE agent and painter Brian Stonehouse, who saw Andrée Borrel and the three other female SOE agents at the Natzweiler-Struthof concentration camp just before their deaths, painted a poignant watercolour of the four women which now hangs in the Special Forces Club in London, England.