Absurdism
Throughout the book, the primary theme is the absurdity of life. This theme begins with the very idea of the construction of the school based on a misunderstanding of the blueprints. Wayside School is thirty stories high with one floor devoted to one grade. Then there is nineteenth floor which was skipped over in the numbering so that even though there is technically a nineteenth floor, it does not exist because the numbering jumps from the 18th to the 20th. The situations and circumstances that each of the many students and faculty members get into are based on a foundation of reality but always stretched to an absurd limit. The point seems to be that this absurdity is not limited merely to the kids or the even the school. The thematic exploration strongly suggests that kids need to be exposed earlier to the reality that adult life and society in the real world is far more absurd than the strict rigidity of lessons and school organization would lead them to expect.
Inequality and Empowerment
The book is structured as a series of short stories that are connected only by the location and the references to multiple characters. Within each story can be found situations which the characters face that vary in the degree of equality. Miss Zarves, for instance, is the teacher occupying the nineteenth floor who must deal with the unfairness of not technically existing even though she and her class clearly do. At the other end of the spectrum is Mrs. Gorf who enjoys the inequality of having the power to turn troublesome children into apples only to this very power literally turned upon her with a mirror so that she accidentally turns herself into an apple and is thereupon eaten. Just as the book suggests thematically that school is a place where children should be prepared for the absurdity of real life, it also strongly submits that despite intentions, equality and empowerment are not fairly divided between the deserving and the undeserving.
Individualism
The students whose stories are told in the book are beyond unusual. For instance, one is revealed, after a particularly absurd tale about multiple raincoats being removed, to actually be a rat. Then there are three different boys named Eric. The book also features a boy named Nancy and a girl named Mac. In other words, the book tells stories about unique individuals some of whom welcome their unusual quality while others actively reject and fight against those qualities. This individuality embodies both the themes of absurdism and inequality as it subtly offers a critique of conformity. Even those characters who fight for conformity are celebrated for their unique qualities. This theme directly confronts the reality of school in which individualism is often harshly treated which urges so many kids to seek to conform to the popularity of the status quo.