The Scuola Normale continued operating despite the Second World War (1940-45), albeit with some limitations and practical difficulties.
In 1940 it participated in the Universal Exposition in Rome for advanced studies and high culture, but dissent towards the regime became more and more manifest among students and professors.
After Mussolini's removal by the Grand Council on the 25th of July 1943, the Scuola Normale remained under German control since it was in the territory of the Republic of Salò.
After the tragic bombardment of Pisa on August 31, the new Scuola Normale director Luigi Russo – threatened with arrest for political dissent – went into hiding in Florence. He was replaced by the mathematician Leonida Tonelli, who defended the library and furnishings of Palazzo dei Cavalieri, which had become a German barracks, by moving the most important collections into the nearby Carthusian monastery in Calci.
After Pisa's liberation on September 2 the Anglo-American army requisitioned the Scuola Normale, so its students and professors were forced to move into the Puteano dormitory. Luigi Russo, reconfirmed as the school's director, continued his efforts to safeguard school and library materials and the activities of the Scuola Normale resumed. On September 25, 1945, the Palazzo was liberated and the restoration of the building began. It was also decided to admit 70 war veterans and partisans as students. For this purpose a plan to augment the school's financial resources beyond state funding was established. The school's patrimony was increased by donations and advantageous purchases; this plan was pursued in the ensuing years as well.
In the post-war years, the Scuola Normale remained substantially the same as it had been under Gentile. In 1959 a “Women's Section” was created, located in the Timpano building, thus allowing women to live inside the school rather than in external housing.