Joan was the third child of Ferdinand II of Aragon and Isabella I of Castile and became heiress in 1500 on the death of her brother and elder sister. She had married Philip of Burgundy, son of the emperor Maximilian, as part of Ferdinand's policy of securing allies against France. They had two sons, Charles, born in 1500, who succeeded as emperor and king of Spain, and Ferdinand, his lieutenant and successor as emperor, and four daughters, all of whom became queens—Eleanor, who married Manuel I of Portugal and then Francis I of France; Elizabeth, who married Christian II of Denmark; Maria, who married Louis II of Hungary; and Catherine, who married John III of Portugal.

Her mental imbalance showed itself in 1502 in the form of extravagant, though justified, jealousy of the unfaithful Philip. On the death of her mother she returned with Philip to Castile and there claimed the regency against her father, who retired to Aragon. The shock of Philip's sudden death (Sept. 25, 1506) intensified her melancholia, and she refused to be parted from his embalmed body. Her father, Ferdinand, returned to take over the regency, and from 1509 she lived under guard at Tordesillas. On Ferdinand's death, her son Charles arrived from the Low Countries and ascertained her unfitness to rule, before taking power. She was legally queen of Spain throughout almost all of his long reign.