Co-ruler of Egypt, inner turmoil

Son of Pharaoh Ptolemy XI 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 and consummation of the marriage to his older sister Cleopatra VII of Egypt (51–30 BC). In October of 50 BC, Ptolemy XII was promoted to senior ruler along with her, although Pothinus acted as regent for him.

In the spring of 48 BC, Ptolemy XII and Pothinus attempted to depose Cleopatra VII due to her increasing status as Queen. Her face appeared on minted coins, for example, while Ptolemy XII's name was omitted on official documents. Ptolemy intended to become sole ruler, with Pothinus acting as the power behind the throne.

Civil war

They managed to force her to flee to Syria, but she soon organized her own army and a civil war began in Egypt. Soon their other sister started to claim the throne as Arsinoe IV (48–47 BC), further complicating the situation.

At this point defeated Roman general Pompey came to Egypt seeking refuge from his pursuing rival Julius Caesar. Initially, Ptolemy XII and Pothinus pretended to have accepted his request, but on September 29, 48 BC, Pothinus himself murdered the general, in hopes of winning favor with Caesar when the victorious general arrived. When Caesar did arrive he was presented with the head of his deceased rival and former ally, but reportedly, instead of being pleased, reacted with disgust and ordered that Pompey's body be located and given a proper Roman funeral. Cleopatra VII proved more successful in winning Caesar's favor and became his lover. Caesar arranged the execution of Pothinus and the official return to the throne of Cleopatra VII, though she had never officially abdicated her marriage to Ptolemy XII.

Still determined to depose Cleopatra VII, Ptolemy XII allied himself with Arsinoe IV. Jointly, they organized the factions of the army loyal to them against those loyal to Cleopatra VII and the relatively small part of his army that had accompanied Caesar to Egypt. The battle between the warring factions occurred in mid-December of 48 BC inside Alexandria itself, which suffered serious damage, including (according to some sources) the burning of some of the buildings which comprised the Library of Alexandria.

The arrival of Roman reinforcements from Pergamum gave the victory to Caesar and Cleopatra VII, forcing Ptolemy XII and Arsinoe IV to flee the city. Ptolemy XII reportedly drowned on January 13, 47 BC while attempting to cross the Nile. Whether he was attempting to flee or was seeking negotiations remains uncertain from sources of the time. Cleopatra VII remained the unchallenged ruler of Egypt, although she named their younger brother Ptolemy XIV of Egypt (47–44 BC) her new co-ruler.