Catherine was born on 7 February 1559 to Queen Jeanne III of Navarre and her husband and co-ruler, Antoine of Bourbon.

Jeanne converted to Calvinism a year after Catherine's birth and declared it the official religion of the Kingdom of Navarre.

She served almost continuously as regent until 1596, where among her other responsibilities, she, a staunch Protestant, hosted Antonio Perez, a famous Spanish Catholic refugee from King Philip II.

Appointed by her brother to sit on his Council as a representative of French Protestant interests in 1598, she set about persuading the Huguenots to agree to the Edict of Nantes.

However, Catherine was a confirmed Calvinist, who refused to convert to Roman Catholicism, whilst her husband was a devout Catholic, and a former member of the Holy League.

Thus, a papal dispensation was required to allow the two to marry, but on 29 December 1598, Pope Clement VIII declared himself opposed to the marriage.