Stephen was born in Landshut, the son of Henry XIII, Duke of Bavaria and Elizabeth of Hungary.
His mother introduced the name Stephen onto the Wittelsbach dynasty with her youngest son.
To reduce the influence of the Wittelsbach, Pope Nicholas IV refused his spiritual career in Salzburg and Stephen became a co-regnant of his brothers.
During the absence of Otto III in Hungary 1305-1308, Stephen was the only governing duke of Lower Bavaria.
Stephen was an enemy of the Habsburgs and died in 1310 during a war against Frederick I of Austria.