Salvator was the eldest son of Archduke Franz Salvator of Austria, Prince of Tuscany and his wife Archduchess Marie Valerie of Austria.

Through his mother, Franz Karl Salvator was a grandson of Emperor Franz Joseph I of Austria, and through his father, he was a great-grandson of Leopold II, Grand Duke of Tuscany.

Franz Karl left the military school as a first lieutenant.

During the First World War, he served as a lieutenant from 1915 to 1918 in operations against Russia, Serbia and Romania.

He lived to see the end of the war and the dissolution of Austria-Hungary in November 1918, but he was already very ill. Franz Karl died at Wallsee Castle on 10 December 1918, at the age of 25, of the Spanish flu, which had been around since the end of October.