A former teacher of grammar and rhetoric, as well as magister scrinorum, Eugenius was an acquaintance of the Frankish magister militum and of the de facto ruler of the Western Roman Empire, Arbogast.
Following the death of Valentinian II, Arbogast, who had probably been the cause of Valentinian II's murder or suicide, elevated Eugenius to the purple (22 August 392). The choice of Eugenius, over proclaiming himself, offered to Arbogast two strong advantages: first, Eugenius, a Roman, was more suitable than Arbogast, a Frank, as an emperor; furthermore, the Roman Senate would have been more likely to have supported Eugenius than Arbogast.
After being installed as Emperor, Eugenius changed the imperial administrators. When Theodosius had left the western half of the empire to Valentinian II, he had put his own men in the highest civil offices, to keep a strong grasp on the whole empire. Eugenius replaced these administrators with others loyal to himself, coming from the senatorial class. Virius Nicomachus Flavianus the Elder became Praetorian Prefect of Italy, his son Nicomachus Flavianus the Younger received the title of Prefect of Rome, while the new praefectus annonae was Numerius Proiectus.
Eugenius was a Christian, and therefore was reluctant to accept a program of imperial support to Polytheism. His men, however, convinced Eugenius to use public money to fund pagan projects, such as the rededication of the Temple of Venus and Rome and the restoration of the Altar of Victory within the Curia (removed by Emperor Gratian). This religious policy created tension with Theodosius and the powerful and influential Bishop Ambrose, who left his see in Milan when the imperial court of Eugenius arrived.
Eugenius was also successful in the military field, notably in the renovation of old alliances with Alamanni and Franks. Arbogast, who was a Frank and had also Alamanni and Frankish soldiers in his ranks, marched to the Rhine frontier, where he impressed and pacified the Germanic tribes by parading his army in front of them.
After his election as emperor, Eugenius sent ambassadors to Theodosius's court, asking for recognition of his election. Theodosius received them, but started to gather troops to defeat Eugenius. Theodosius also promoted his eight-year-old son Honorius to the rank of "Augustus" of the West in January 393.
Theodosius then moved from Constantinople with his army, and met Eugenius and Arbogast in the Battle of the Frigidus (Vipava Valley, Slovenia) on 6 September 394. The bloody battle lasted two days, and was marked by unusual astronomical and meteorological events, but in the end Theodosius won. Arbogast immediately committed suicide after the defeat, while Eugenius was held for execution as a criminal, his head afterward being displayed in Theodosius' camp.
The reign of Eugenius marked the end of an era and the beginning of a new one. Five months later Theodosius died, dividing his empire between his two sons. This had happened many times before in the previous two centuries, but this time it was to be final – the Roman Empire never reunited, even under Leo I the Thracian (when there was no Western Emperor for some periods), and soon after his reign, the western half fell.
Eugenius also represented the last opportunity for the pagans, with the senatorial class, to oppose the Christianization of the Empire. The Battle of the Frigidus was part of a trend towards using increasing percentages of barbarian troops, especially in the west, where it led to the weakening of the Empire itself.