[6][1] Both he and his younger brother Sextus Pompey grew up in the shadow of their father, one of Rome's best generals and not originally a conservative politician who drifted to the more traditional faction when Julius Caesar became a threat.

When Caesar crossed the Rubicon in 49 BC, thus starting a civil war, Gnaeus followed his father in their escape to the East, as did most of the conservative senators.

Gnaeus fled to the Balearic Islands, where he was joined by Sextus following Caesar's defeat of Metellus Scipio and Cato, who subsequently committed suicide, at the Battle of Thapsus in 46 BC.

[5][7] His younger brother Sextus Pompeius was able to keep one step ahead of his enemies, and survived his brother for another decade by establishing a semi-independent kingdom in Sicily with a powerful naval fleet, becoming so powerful he had to be accommodated by the Second Triumvirate until Augustus sent his general Marcus Agrippa who fought the Bellum Siculum with Sextus who was eventually defeated and executed.

Gnaeus Pompeius married Claudia Pulcra, daughter of Appius Claudius Pulcher and sister of Marcus Junius Brutus' first wife, who survived him; they had no children.