Her uncle John of Foix, appealing to the Salic Law alien to the Kingdom of Navarre, claimed the throne and ignited a civil war (1483–1492) that reignited the old conflict of the Beaumont-Agramont parties.

In 1484, hard pressed by ambitions over the throne of Navarre, Magdalena of Valois decided to marry 15-year-old Catherine to John of Albret, hailing from a noble family in western Gascony.

[2] The wedding took place at the Notre Dâme Cathedral of Lescar in 1486,[3]: 75  but the coronation of the young couple in Pamplona was deferred until 1494, after a fleeting peace treaty with Louis of Beaumont, Count of Lerín, and Catherine's granduncle, King Ferdinand II of Aragon, was signed.

Catherine was described as “very mature, she had great courage, prudence and the magnanimity and always worked with all fidelity at the royal pledges to help the King, her husband, in the government as it ran to both their account.”[4] In 1504, she made her will, confirming her son Henry's right to succeed her and expressing her wish to be buried at the Cathedral of Pamplona—ultimately both she and John were interred in Lescar.

[3]: 75 On 23 March 1513, the Cortes of Navarre reunited in Pamplona (Iruñea in Basque), greatly reduced to the pro-Spanish Beaumont party, and pledged allegiance to Ferdinand in exchange for his loyalty to the Navarrese laws.

From 1512 to her death in 1517, Catherine was actual queen only in some areas of Basse-Navarre, or Lower Navarre, north of the Pyrenees, but her domains extended to the contiguous Principality of Bearn and other lands.