Koja's novels and short stories frequently concern characters who have been in some way marginalized by society, often focusing on the transcendence and/or disintegration which proceeds from this social isolation (as in The Cipher, Bad Brains, "Teratisms," The Blue Mirror, etc.).

[4] Author Mike Thorn described her novel Dark Factory as "a daring work of multisensory immersion.

[citation needed] Koja's work is influenced by Shirley Jackson, Flannery O'Connor, Carter Scholz, and Sylvia Plath.

Paula Rohrlick, writing in Kliatt, praised Straydog as a "short, swift read … packed full of emotion."

A critic for Kirkus Reviews added that "fans of tales about teen writers, or stories with animal themes, will pant after this."

A contributor to Publishers Weekly described Straydog as a "solid if sometimes familiar tale of a high school misfit" that presents teen readers with a "compelling and sympathetic" protagonist in Rachel.

Farida S. Dowler, writing in School Library Journal, noted that Koja's presentation of Rachel's growing "friendship with Griffin has romantic tension, but transcends high-school stereotypes," while in The Horn Book Jennifer M. Brabander concluded that the novel is a "fast but semi-sophisticated read for teens who haven't outgrown dog stories.

"[citation needed] Praising The Blue Mirror as an "eerie, psychologically gripping urban tale" similar to the work of author Francesca Lia Block, a Publishers Weekly reviewer added that in her story "Koja explores the confusion between infatuation and real love—in all its cruelty and its redemptive powers."

Of the novel, Koja noted on her website: "The Blue Mirror is concerned with vision, the way we see—or sometimes refuse to see—what's right in front of us, and what can happen when we open our eyes.