Rupert was born in Prague, Bohemia (now the Czech Republic), during a tumultuous period of European history. His parents were Frederick V, Elector Palatine, and Elizabeth Stuart, daughter of King James VI and I of Scotland and England. His birth occurred shortly before his father was crowned King of Bohemia, a move that ignited the Thirty Years' War.

The death of his father, Frederick V, in exile, shaped young Rupert's life, fueling a desire to restore his family's Palatinate lands. He received a military education, gaining early combat experience in the latter stages of the Thirty Years' War alongside his brother, Prince Charles Louis. His bravery and tactical skills became evident, earning him a reputation as a formidable military leader at a young age.