Ptolemy XIII and Pothinus managed to force Cleopatra to flee to Syria, but she soon organized her own army and a civil war began in Egypt.

[4] Upon the arrival of Roman reinforcements, the Battle of the Nile (47 BC) ensued and resulted in a victory for Caesar and Cleopatra, forcing Ptolemy XIII to flee the city.

Ptolemy and his fight with Caesar and Cleopatra for control of Egypt also feature in the HBO TV series Rome episode "Caesarion".

Ptolemy's civil war with Cleopatra figures prominently in the 2017 historical video game Assassin's Creed Origins, in which he is presented as a weak puppet ruler to the Order of Ancients who drove him to depose his sister.

At the end of the war, main character Aya draws an arrow to kill him, but holds back as his boat is attacked by crocodiles, causing him to fall into the river and drown.