He was the son of Rudolf I, Duke of Bavaria and Mechtild of Nassau, the daughter of Adolf of Nassau-Weilburg, King of Germany.

With the death of his brother, Rudolf II, on 4 October 1353, he inherited his domains and became sole Count for the territory, whereas they had previously shared that privilege.

The Golden Bull of 1356 guaranteed the Palatinate the right of participating in the election of the Holy Roman Emperor.

Rupert was married twice: firstly to Elisabeth, Countess of Namur (daughter of John I, Marquis of Namur), secondly to Beatrix of Jülich-Berg, the great-granddaughter of his elder brother Adolf, Count Palatine of the Rhine.

He was succeeded by his nephew, Rupert II, Elector Palatine, grandfather of his second wife.