A Tale of the Secret Saint follows a young woman named Fia Ruud, who is the least talented member of a family of knights but remains determined to follow in their footsteps. During what was meant to be a simple test to prove her worth by slaying a small demon, she instead finds herself facing a dragon. The encounter proves deadly, and as Fia teeters on the brink of death, her life flashes before her eyes, triggering the sudden recollection of a previous existence. She remembers her past life as a legendary and immensely powerful Great Saint who, three hundred years prior, helped a hero defeat the Demon King. That life, however, ended in pain and betrayal, as she was abandoned and tortured after her power was spent. This traumatic memory is accompanied by a dire threat from the Demon King’s right-hand man, who swore to find and kill her if she was ever reborn as a Saint. With her past life's holy magic rekindled, Fia faces an impossible situation. Her new power could make her the knight she has always dreamed of being, but revealing it would expose her as a Saint and put her in mortal danger. Terrified of a repeat of her former fate, she vows to hide her identity and live a quiet life as an ordinary knight, a resolve that is constantly tested by her compassionate nature and the sheer usefulness of her abilities.

The story is set in a fantasy world where humanity is on the brink of extinction, making Saints highly revered and crucial figures. The narrative centers on Fia's double life as she joins the Knight Brigades, hoping to blend in. Key figures in her new life include Zavilia, a powerful black dragon she forms a contract with after healing it, who often takes the form of a small, weak-looking monster to help keep her secret; Saviz Nav, the captain of the Knight Brigades; and Cyril Sutherland, the captain of the First Knight Brigade. A significant narrative arc involves Fia joining a learning expedition with the Fourth Monster Tamer Brigade, where her power nearly gets exposed. She also must deal with the constant scrutiny of those around her who become curious about her abilities and the small dragon by her side. As she navigates the dangers of knighthood, the trauma of her past life looms large, particularly the memory of being killed for her power, creating the central tension between her desire to help others and her desperate need to remain hidden.