The early chapters of the novel deal with Tom Brown's childhood at his home in the Vale of White Horse. Tom Brown's first school year was at a local school. His second year started at a private school, but due to an epidemic of fever in the area, all the school's boys were sent home, and Tom was transferred mid-term to Rugby School, where he made acquaintance with the adults and boys who lived at the school and in its environs. On his arrival at Rugby, Tom Brown is looked after by a more experienced classmate, Harry "Scud" East. Soon after, Tom and East become the targets of a bully named Flashman.
In the second half of the book, Dr. Thomas Arnold, the historical headmaster of the school at the time, gives Tom the care of George Arthur, a frail, pious, academically brilliant, gauche, and sensitive new boy.
Parodies include "Tompkinson's Schooldays" in Ripping Yarns, "Tim Brown's Schooldays" in I'm Sorry I'll Read That Again, the first episode of Bleak Expectations and the boarding school sequence in the Discworld novel Pyramids.
Tom Brown's Schooldays provides examples of:
- Aristocrats Are Evil - Most are not, but Flashman and his father embody the worse side of the aristocracy.
- Author Tract - Reportedly, when people told Hughes that the book would have been more enjoyable if it were less preachy, he replied that as far as he was concerned the opportunity to preach was the whole point of the exercise. It should be noted that the preaching is strongest in the second half of the book, which is rarely adapted into film or TV.
- Baseball Episode - Make that Cricket. These are English boys, after all.
- Boarding School - Rugby, a Real Life public school
- Boarding School of Horrors
- The Bully - Flashman
- Clear My Name
- Evil Poacher
- Historical-Domain Character - Dr. Arnold, the actual headmaster of the real Rugby School at the time the novel is set.
- Period Piece - Set about 25 years before it was written (ie. about the time the author was at school).
- Quintessential British Gentleman - To various degrees, most of the upper-class British characters that form the focus of the story.
- Tuckerization - Several of the characters are based on people the author knew in his own schooldays.