Francis Ferdinand was the eldest son of the archduke Charles Louis, who was the brother of the emperor Francis Joseph. The death of the heir apparent, the archduke Rudolf, in 1889, made Francis Ferdinand next in succession to the Austro-Hungarian throne after his father, who died in 1896. But because of Francis Ferdinand's ill health in the 1890s, his younger brother Otto was regarded as more likely to succeed, a possibility that deeply embittered Francis Ferdinand. His desire to marry Sophie, countess von Chotek, a lady-in-waiting, brought him into sharp conflict with the emperor and the court. Only after renouncing his future children's rights to the throne was the morganatic marriage allowed in 1900.

In foreign affairs he tried, without endangering the alliance with Germany, to restore Austro-Russian understanding. At home he thought of political reforms that would have strengthened the position of the crown and weakened that of the Magyars against the other nationalities in Hungary. His plans were based on the realization that any nationalistic policy pursued by one section of the population would endanger the multinational Habsburg empire. His relationship with Francis Joseph was exacerbated by his continuous pressure on the emperor, who in his later years left affairs to take care of themselves but sharply resented any interference with his prerogative. From 1906 onward Francis Ferdinand's influence in military matters grew, and in 1913 he became inspector general of the army.

In June 1914 he and his wife were assassinated by the Serb nationalist Gavrilo Princip (Princip, Gavrilo) at Sarajevo; a month later World War I began with Austria's declaration of war against Serbia.