When her father died five days before her fourth birthday, Eleanor's brother Afonso V succeeded him as king with her mother as regent.

The following March, her mother gave birth to another daughter, Joan, who would become the notorious wife of Henry IV of Castile.

In 1440, Eleanor's mother was forced to go into exile in Castile after losing litigation against her brother-in-law Peter, Duke of Coimbra, for the regency of the young King Afonso.

Eleanor was also suggested as a marriage partner for Louis, Dauphin of France, the eldest son of King Charles VII, but she herself preferred to marry Frederick, because a match with him would give her the title of empress instead of queen.

During her marriage to Frederick III, she had five children: Eleanor died in Wiener Neustadt on 3 September 1467 and is buried in the Cistercian abbey Neukloster, where her tombstone is still prominent in the church's apse.