The modern island was formed probably 4.5 to 5 million years ago, and has been inhabited since the Stone Age. Later, it was probably an Etruscan military stronghold. Under the Roman dominion, Aegilium Insula or Igillia Insula it was an important base in the Tyrrhenian Sea, and was cited briefly by Julius Caesar in his De Bello Civili,by Pliny, by Pomponius Mela, and by the fifth-century AD poet Rutilius Claudius Namatianus, who celebrated Igilium’s successful repulse of the Getae and safe harbor for Romans, in a time when Igilium’s slopes were still wooded.
In 805, the island was donated by Charlemagne to the abbey of the Tre Fontane in Rome, and was later successively a possession of the Aldobrandeschi, Pannocchieschi, Caetani, and Orsini families, and of the municipality of Perugia. In 1241, the Sicilian and Pisan fleet of Emperor Frederick II destroyed a Genoese fleet in the Battle of Giglio. From 1264, Isola del Giglio was a Pisan dominion, from which it passed to the Medici family. It suffered several Saracen attacks, which ended only in 1799.
On 14 June 1646, Grand Admiral Jean Armand de Maillé-Brézé was killed at the Battle of Orbetello, at sunset on his flagship the Grand Saint Louis.
Alongside its history, the island was always renowned for its mineral ore: many columns and buildings in Rome were built with the Gigliese granite.