Johnson was born in South Dakota and raised in Arizona. He earned a BA in Journalism from Arizona State University in 1992; a MFA from the writing program at McNeese State University, where he was a classmate of the writer Neil Connelly, in 1996; and a PhD in English from Florida State University in 2000. Johnson is currently a San Francisco writer and Jones Lecturer at Stanford University. He is a co-editor, along with Tom Kealey, of the Stanford Graphic Novel Project.

Johnson is the author of the short-story collection Emporium and the novel Parasites Like Us, which won a California Book Award in 2003. His work has been published in Esquire, Harper's Magazine, Tin House and The Paris Review, as well as Best New American Voices and The Best American Short Stories. His work has been translated into French, Japanese, Catalan, German, Croatian and Serbian and focuses on characters at the edge of society for whom isolation and disconnection are nearly permanent conditions. Michiko Kakutani, writing in The New York Times, described the central theme "running through his tales is also a melancholy melody of longing and loss: a Salingeresqe sense of adolescent alienation and confusion, combined with an acute awareness of the randomness of life and the difficulty of making and sustaining connections."A strain of absurdity also runs through is work, causing it to be described as "a funky new science fiction that was part irony and part pure dread." "Teen Sniper" is about young sniper prodigy enlisted by the Palo Alto police department to suppress the disgruntled workers of Silicon Valley. "The Canadanaut" follows a remote team of Canadian weapons developers who race to beat the Americans to the Moon. Johnson is currently at work on a novel set in North Korea.

Johnson has received a Whiting Writers' Award, a National Endowment for the Arts Fellowship, a Swarthout Writing Award, a Kingsbury Fellowship and a Stegner Fellowship. He was named Debut Writer of the Year in 2002 by Amazon.com, and in 2003 he was selected for the Barnes & Noble Discover Great New Writers series. He was nominated for a Young Lions Award from the New York Public Library and received scholarships from the Bread Loaf and Sewanee writers' conferences. In 2010, he won the Gina Berriault Literary Award.

• Emporium (story collection) (2002)
• Parasites Like Us (novel) (2003)

Story publications

• "Hurricanes Anonymous" in Tin House
• "The Denti-Vision Satellite" in Ninth Letter
• "Cliff Gods of Acapulco" in Esquire
• "The History of Cancer" in Hayden's Ferry Review
• "Watertables" in The Missouri Review
• "The Canadanaut" in The Paris Review
• "Your Own Backyard" in The Southeast Review
• "The Death-Dealing Cassini Satellite" in New England Review
• "Teen Sniper" in Harper's Magazine
• "Trauma Plate" in The Virginia Quarterly Review