Disputed by the two halves of the Empire in the following years, the Diocese of Pannonia was one of the two dioceses in the eastern quarters of the Tetrarchy not belonging to the cultural Greek half of the empire (the other was Dacia), and so it was transferred back to the Western Empire at the death of Theodosius I in 395 and was joined to the Prefecture of Italy as the Diocese of Illyricum.

In 425 Galla Placidia gave the diocese of Illyricum to Eastern Emperor Theodosius II.

Pannonia was lost to the Huns in the 440s, although Dalmatia was retained by the Western Empire until c. 480.

The Ostrogoth king of Italy Theodoric the Great conquered Pannonia in the late 5th century, possibly reestablishing the diocese.

In the 9th century, Diocese of Pannonia was also a name of the ecclesiastical territory of the Christian church whose archbishop was Saint Methodius.