He was son of king Antiochus X Eusebes and the Ptolemaic princess Cleopatra Selene, who acted as regent for the boy after his father's death sometime between 92 and 85 BC. Some time after Tigranes had conquered Syria (83 BC), she travelled to Rome to have her sons recognized as kings of Egypt, but to no avail. They were there between at least between 75 BC and 73 BC; recognized as "Kings of Syria", and "maintained a royal state" (Bevan, p. 263). Selene was eventually captured and killed by Tigranes, but after the latter's defeat by Pompey, the residents of Antioch hailed Antiochus XIII as king, and Lucius Lucullus approved his appointment as client ruler of Syria (69 BC).
In 64 BC, Pompey had him deposed and killed by an Arab chieftain Sampsiceramus (Shemashgeram). Antiochus' death is traditionally said to have ended the Seleucid dynasty, but he was survived by Philip II Philoromaeus for a short time.