The novel is set on the Waller plantation in the Southern United States in the 1850s. The narrator and protagonist of the story is a young female African-American slave named Sarny. Sarny first sees Nightjohn when he is brought to the plantation with a chain around his neck, his body covered in scars. He had escaped north to freedom, but he came back - came back to teach reading.
Knowing that the penalty for reading is dismemberment, John still returned to slavery to teach others how to read. Twelve-year-old Sarny is willing to learn. So, at night and whenever he has the chance, John begins teaching Sarny the letters of the alphabet. After teaching her 7 letters (A to G), Waller catches Sarny writing in the dirt and punishes John for teaching her by cutting off the toes from each of his feet. But then after three days of recuperating, John runs and makes it to freedom.
He later returns to fetch Sarny and take her to "pit school" in the night, where she sees and learns what a catalog is, learns the rest of the letters, and has acquired great knowledge - something no one can take away from her. Since John comes at night, he is called Nightjohn. This book was followed by a sequel called Sarny, a Life Remembered in 1998.