The book tells the story of Burroughs's bizarre childhood life after his mother, a chain-smoking aspiring poet, sent him to live with her psychiatrist.

[2] Running with Scissors covers the period of Burroughs' adolescent years, beginning at age 12 after a brief overview of his life as a child.

Burroughs spends his early childhood in a clean and orderly home, obsessing over his clothes, hair, accessories, and having great potential, with his parents constantly fighting in the background.

Rules are practically nonexistent and children of all ages do whatever they please, such as having sex, smoking cigarettes and cannabis, and rebelling against authority figures.

However, the dysfunctional issues that occur in the Finch family are outdone by the psychotic episodes frequently experienced by Burroughs' mother.

It is filthy, with cockroaches roaming around the uncleaned dishes, Christmas trees left up year-round, stairs up which Burroughs is afraid to walk because he thinks that they will collapse under him, and nothing off limits.

Eventually, Finch comes to believe that God is communicating with him through his feces and develops a form of divination to try and decipher these messages.

Burroughs forms a close relationship with Finch's daughter, Natalie, who is one year older than he is, even though he dislikes her at the beginning of the book.

At the end of the book, when Burroughs is living in his own apartment with Natalie, he is asked to choose between his mother and Finch when she accuses the doctor of raping her in a motel to cure her of one of her psychotic episodes.

[4] In 2005, the family of Dr. Rodolph H. Turcotte (1919–2000) of Massachusetts filed suit against Burroughs and his publisher, alleging defamation of character and invasion of privacy.

Burroughs defended his work as "entirely accurate", but agreed to call the work a "book" (instead of a "memoir") in the author's note, to alter the acknowledgments page in future editions to recognize the Turcotte family's conflicting memories of described events, and express regret for "any unintentional harm" to the Turcotte family.