Gnaeus Pompeius was the elder son of Pompey the Great (Gnaeus Pompeius Magnus) by his third wife, Mucia Tertia. 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. Pompey's army lost the Battle of Pharsalus in 48 BC, and Pompey himself had to run for his life, only to be murdered in Egypt on 29 September the same year.
After the murder, Gnaeus and his brother Sextus joined the resistance against Caesar in the Africa Province. Together with Metellus Scipio, Cato the Younger and other senators, they prepared to oppose Caesar and his army to the end. Caesar defeated Metellus Scipio and Cato, who subsequently committed suicide, at the Battle of Thapsus in 46 BC. Gnaeus escaped, this time to the Balearic Islands, where he joined Sextus. Together with Titus Labienus, former general in Caesar's army, the Pompey brothers crossed over to Hispania (the Iberian Peninsula, comprising modern Spain and Portugal), where they raised yet another army.
Caesar soon followed and, on 17 March 45 BC, the armies met in the Battle of Munda. Both armies were large and led by able generals. The battle was closely fought, but eventually a cavalry charge by Caesar turned events to his side. In the battle and the panicked escape that followed, Titus Labienus and an estimated 30,000 men of the Pompeian side died. Gnaeus and Sextus managed to escape another time but supporters were difficult to find. It was by now clear Caesar had won the civil war. Within a few weeks, Gnaeus Pompeius was cornered and killed by Lucius Caesennius Lento. Sextus Pompeius was able to keep one step ahead of his enemies, and survived his brother for another decade.
Gnaeus Pompeius married Claudia Pulchra, who survived him; they had no children.