Gnaeus Pompeius was the oldest son of Pompey the Great (Gnaeus Pompeius Magnus) by his third wife, Mucia Tertia. His younger brother was Sextus Pompeius, from the same mother. Both boys grew up in the shade of his father, one of Rome's best generals and originally non-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 September 29 of the same year.
After the murder, Gnaeus and his brother Sextus joined resistance against Caesar in the Africa provinces. Together with Metellus Scipio, Cato the younger and other senators, they prepared to oppose Caesar and his army to the end. Caesar won the first battle at (Thapsus) in 46 BC, against Metellus Scipio and Cato, who committed suicide. Gnaeus escaped once again, this time to the Balearic Islands, where he joined Sextus. Together with Titus Labienus, former general in Caesar's army, the Pompey brothers cross over to Hispania provinces, where they raised yet another army.
Caesar and his legions soon follow and, on March 17, 45 BC the armies met in the battle of Munda. Both armies were very strong in numbers and led by able generals. The battle was heavily fought, but eventually a cavalry charge by Caesar turned the events to his side. Titus Labienus and an estimated 30,000 men of the Pompeian side died not only in the battle, but also in the panicked escape that followed. Gnaeus and Sextus managed to escape once again. However, this time, supporters were difficult to find because with Munda, it was clear Caesar had won the civil war. Within a few weeks, Gnaeus Pompeius was caught and executed for treason. Sextus Pompeius was able to keep one step ahead of his enemies, and outlived his older brother for a number of years.