Son of Pharaoh Ptolemy XII of Egypt (80-58 BC and 55-51 BC), he succeeded his father in the spring of 51 BC as co-ruler of Egypt by his marriage to his older sister Cleopatra VII of Egypt (69-30 BC).
In the spring of 48 BC, Ptolemy XIII and Pothinus attempted to depose Cleopatra VII due to her increasing status as Queen.