During the Roman civil war of 49–45 , Cornificius sided with Julius Caesar against Gnaeus Pompeius. As "quaestor pro praetore" for Illyricum in 48 BC, he recovered the province and defended it against the attacks of Pompeius' fleet. In 46, he was sent to Cilicia, probably as "legatus pro praetore", and then to Syria, where he prosecuted the war against Quintus Caecilius Bassus. In 45 BC, he was made a "praetor" and in the summer of 44 BC, after the assassination of Caesar, he was appointed governor of the province of Africa Vetus by the senate.