On 17 January 395, Theodosius I succumbed to death. Arcadius succeeded him in the Eastern Roman Empire and Honorius in the Western Roman Empire. Arcadius was effectively placed under the control of Rufinus, Praetorian prefect of the East. Rufinus reportedly intended to marry his daughter to Arcadius and establish his own relation to the Theodosian dynasty.
However, while Rufinus was distracted by a conflict with the magister militum of the West, the wedding of Eudoxia to Arcadius was orchestrated by Eutropius, one of the eunuch officials serving in the Great Palace of Constantinople. The marriage took place on 27 April 395, without the knowledge or consent of Rufinus. For Eutropius it was an attempt to increase his own influence over the emperor and hopefully ensure the loyalty of the new empress to himself. Zosimus reports that Arcadius was also influenced by the extraordinary beauty of his bride. Arcadius was approximately eighteen years old and Eudoxia may be presumed to be of an equivalent age.
The extent of her influence at matters of court and state has been a matter of debate among historians. Philostorgius considers her to be more intelligent than her husband but comments on her “barbarian arrogance”. Zosimus considers her strong-willed but ultimately manipulated by eunuchs at court and the women of her environment. Barbarians and Bishops: Army, Church, and State in the Age of Arcadius and Chrysostom (1990) by J. W. H. G. Liebeschuetz considers her influence overestimated in primary sources while The Cambridge Ancient History XIII. The Late Empire A.D. 337-425 (1998) reports her dominating the government between 400 and her death in 404.
In 403, Simplicius, Prefect of Constantinople, erected a statue dedicated to her on a column of porphyry and a base of marble. Arcadius renamed the town of Selymbria Eudoxiopolis after her, though this name did not survive.