Stephen was the son of Eudokia Ingerina and, officially, Emperor Basil I. However, at the time when he was conceived, Eudokia was the mistress of Emperor Michael III. Consequently, it is possible or even probable that like his older brother Leo VI the Wise, Stephen was actually Michael's son.
Castrated by Basil I, Stephen became a monk and was designated for a career in the church since his childhood. In 886 his brother, the new Emperor Leo VI, dismissed the Patriarch Photios and appointed the 19-year old Stephen as patriarch in his stead.
As patriarch Stephen participated in the ceremonial reburial of Michael III by Leo VI in the imperial mausoleum attached to the Church of the Holy Apostles in Constantinople. There are no important events associated with Stephen's patriarchate and the patriarch, who acquired a reputation for piety, died in May 893.