Louis Auchincloss's The Rector of Justin tells the story of Frank Prescott, the founder of a New England preparatory school for boys—much like the one Auchincloss himself attended as a youth (Groton School). His story is seen through the eyes of several different narrators, each with their own unique perspectives on his life, character, and motivations.

Francis "Frank" Prescott is the founder of St. Justin Martyr, an exclusive school for boys with more than half a century's worth of renown. He is proud, often stubborn, and sometimes rash; but he genuinely loves his school and his students, and is regarded by most with the utmost respect.

His tale unfolds through the perspectives of: Brian Aspinwall, a student who hasn't been enlisted to fight in World War II because of his failing health; the memoirs of Prescott's oldest friend; his rebellious daughter; and the recollections of one of his first students who went on to become a trustee of the school. At the beginning of the story, Prescott is well into his eighties.

Aspinwall, the principal narrator of the story, begins to write his thoughts on and observations of Prescott in his journal. Eventually, he decides that he ought to write a proper biography about him. He begins to arduously and meticulously research and document Prescott's life.

Born in 1860 in New England, Prescott lost both his parents: his father to war and his mother to disease. Prescott went on to study at Oxford and, while there, was inspired by British public schooling to start something similar in America. He returned to America in 1881, worked a regular job at a railroad for a while, and then married a woman named Harriet Winslow. The couple had three daughters, but Prescott's single-minded ambition to build the perfect boys' preparatory school often took him away from his family life.

The story deals with Prescott's ambition and perfectionism, his Episcopalian beliefs, and, above all, the legacy he sacrificed almost everything to create.