Rupert was born in Prague, Bohemia (modern-day Czech Republic). His parents were Frederick V, Elector Palatine, and Elizabeth Stuart, daughter of King James VI of Scotland (James I of England). His birth coincided with a tumultuous period as his father briefly held the throne of Bohemia.

Frederick V's forces were defeated at the Battle of White Mountain, leading to the loss of the Bohemian throne and the family's exile. This defeat marked the beginning of the Thirty Years' War for the Palatinate and fundamentally shaped Rupert's future.

The family settled in The Hague, Netherlands, under the protection of Rupert's uncle, Prince Maurice of Orange. Rupert spent his childhood and adolescence largely in the Dutch Republic, receiving a Calvinist education.

Rupert received a thorough education, learning languages (including English, German, French, and Latin), mathematics, and military tactics. He showed an early aptitude for horsemanship and military matters, likely influenced by his exposure to Dutch military traditions.

Rupert began gaining practical military experience, observing and participating in campaigns during the Eighty Years' War (Dutch Revolt). This early exposure laid the foundation for his later, more prominent, military commands.

The death of his father, Frederick V, solidified Rupert's commitment to restoring the Palatinate to his family. He felt a deep sense of duty to avenge his father's loss and reclaim his birthright.

Rupert formally joined the Dutch army under Prince Frederick Henry of Orange. He actively participated in military operations against the Spanish.