In Caesar's Gallic wars the Thirteenth was present in the battle against the Nervians and the siege of Gergovia. When the senate refused Caesar his second consulship and civil war was about to begin, the Thirteenth was the legion that accompanied Caesar across the Rubicon river and into Italy. They remained faithfull to Caesar in the civil against Pompey, being present in the battle of Munda (45 BC) and in the African campaign. In 45 BC Caesar disbanded the legion, giving the veterans farmlands in Italy.
In 41 BC the legion is reconstituted by Augustus to deal with Pompey's sons rebellion in Sicily. After the war against Marcus Antonius and the battle of Actium, the Thirteenth was reinforced with veteran legionaries from other legions and acquired the cognomen Gemina. Augustus then sent this legion to Illyricum, a Roman province in the Adriatic Sea. In 16 BC they were transferred to Pannonia, where they dealt with local rebellions.
After the disaster of the battle of the Teutoburg Forest in 9 AD, the legion was sent as reinforcements to Germania Superior to prevent further attacks from the Germanic tribes. Emperor Claudius sent them back to Pannonia around 45 AD.
In the year of the four emperors, XIII Gemina supported Otho, one of the defeated emperors. In 89 Domitian transferred the legion to Dacia to garrison the province from their camp in Vienna. They remained in this camp until the 5th century, although it is possible that the legion, or sub-units of it, participated in several foreign campaigns.