Juárez was born on March 21, 1806, in the Oaxaca village of San Pablo Gueletao. His parents, members of the Zapotec tribe prevalent in Oaxaca, were small farmers. When he came to Oaxaca City at the age of thirteen, he could neither read, write nor speak Spanish. His destination was the house of the Maza family, where his sister worked as a servant. Sr. Maza, head of the household, not only took in the boy but showed an interest in his development.

A friend of Maza was Antonio Salanueva, a devout Catholic and lay member of the Franciscan order. Salanueva taught the boy reading, writing, arithmetic, Spanish grammar and bookbinding. Both older men were so impressed with Benito's aptitude that they sent him to the Franciscan seminary in Oaxaca with the idea of turning him into a priest. Though young Juárez immersed himself in the study of Aquinas and other great Catholic philosophers, he decided in the end that his career lay in law rather than religion. Graduating from the seminary in 1827, he entered the Institute of Science and Art, emerging with a law degree in 1834.

During this period he was reading works by the rationalist philosophers of the Enlightenment. In the end, he became completely imbued with their secular doctrines and abandoned the Catholic faith of his early days.