Unlike many women of her era, Stanton was formally educated. She attended Johnstown Academy, where she studied Latin, Greek and mathematics until the age of 16. At the Academy, she enjoyed being in co-ed classes. She competed intellectually and academically with boys her age and older. She did this very successfully, winning several academic awards and honors while a student in Johnstown.
In her memoir, Stanton credits the Cadys' neighbor, Rev. Simon Hosack with strongly encouraging her intellectual development and academic abilities at a time when she felt they were undervalued by her father. Writing of her brother Eleazar's death in 1826, Stanton remembers trying to comfort her father. She told him that she would try to be all her brother had been. He exclaimed, "Oh, my daughter, I wish you were a boy!" Her father's response devastated Stanton. Stanton concluded that her father valued boys above girls. Stanton confided her disappointment to Hosack. His firm belief in her abilities counteracted her father's disparagement. Hosack taught Stanton Greek, encouraged her to read widely, and ultimately bequeathed his Greek lexicon and other books to her. His belief in her intellectual abilities buttressed Stanton's belief in her own wide-ranging abilities and prowess.
Upon graduation from Johnstown Academy, Stanton experienced her first tastes of sexual discrimination. Stanton watched with dismay as the young men graduating with her, many of whom she had surpassed academically, went on to Union College. In 1830, Union College only admitted men. Stanton's only option was to enroll in the Troy Female Seminary in Troy, New York.
Early in her days at Troy, Stanton encountered Charles Grandison Finney, an evangelical preacher and revivalist. After hearing Finney speak, Stanton became terrified of her own possible damnation, "Fear of judgment seized my soul. Visions of the lost haunted my dreams. Mental anguish prostrated my health. Dethronement of my reason was apprehended by my friends." Stanton credits her father and brother-in-law, Edward Bayard, with removing her from the situation. After taking her on a rejuvenating trip to Niagara Falls, they finally restored her reason and sense of balance. She never returned to organized Christianity. After this experience she maintained that logic and a humane sense of ethics were the best guides to thought and behavior.