Bank of France Governor Pierre-Eugène Fournier was named head of SNCF on 6 September 1940. He knew the French rail system well: his 1929 report on the industry's business model and finances had led to SNCF's creation in 1937. He agreed to head the company under the armistice agreement, which divided France into occupied and unoccupied zones. In occupied France, transport was placed under German control, while the French State had direct authority over SNCF in the unoccupied zone.

Mr Fournier stepped down in August 1946. By the end of World War II, Allied bombings and sabotage by resistance fighters had destroyed three-quarters of the rail network, and 10,000 railway workers had lost their lives.

In November 2010, SNCF apologized for the consequences of its actions while under requisition. During the war, SNCF wagons transported some 76,000 men, women and children—classified as Jews under the laws of Vichy France—to Germany, where they were sent to concentration camps.