De' Pazzi was born at Florence, Italy, on April 2, 1566,to Camillo di Geri de' Pazzi, a member of one of the wealthiest and most distinguished noble families of Renaissance Florence, and Maria Buondelmonti. She was christened Caterina, but in the family was called Lucrezia, out of respect for her paternal grandmother, Lucrezia Mannucci.
At the age of nine de' Pazzi was taught how to meditate by the family chaplain, using a then-recently-published work explaining how one should meditate on the Passion of Christ. Years later, this book was one of the items she brought with her to the monastery.Around the age of nine is also when de' Pazzi began practicing mortification of the flesh through self-flagellation, wearing a barbed metal cilice, and wearing a home-made crown of thorns. She received her First Communion at the then-early age of 10 and made a vow of virginity the same year.She experienced her first ecstasy when she was only twelve, in her mother's presence. From then on, she continued to exhibit what she considered to be many varied mystical experiences.
In 1580, at age fourteen, de' Pazzi was sent by her father to be educated at a monastery of nuns of the Order of Malta, but she was soon recalled to wed a young nobleman. Caterina advised her father of her vow, and he eventually relented and allowed her to enter monastic life. She chose the Carmelite monastery of Santa Maria degli Angeli in Florence because the rule there allowed her to receive Holy Communion daily. On January 30, 1583, she was accepted as a novice by that community, and took the religious name of Sister Mary Magdalene.