• "Roadkill" (Tales of the Unanticipated #3, 1988)
• "FERATA" (Pulphouse: The Hardback Magazine #1, Fall 1988)
• "Wolf Trapping" (The Twilight Zone Magazine, April 1989)
• "Solving the Homeless Problem" (Pulphouse: The Hardback Magazine #8, Summer 1990)
• "Hera's Madness" (Weird Tales #298, Fall 1990)
• "I [heart] my [dogface]" (Tales of the Unanticipated #8, 1991)
• "Ursula Redux" (with Phillip C. Jennings) (Amazing Stories, March 1991)
• "Canine Intervention" (Pulphouse: The Hardback Magazine #11, Spring 1991)
• "Questing" (Tales of the Unanticipated #10, 1991)
• "Last Dance at Dante's" (Tales of the Unanticipated #11, 1993)
• "The Emperor's New Prose" (Swashbuckling Editor Stories, 1993)
• "Schrödinger's Cathouse" (The Magazine of Fantasy and Science Fiction, March 1993)
• "Fox Magic", (Asimov's, December 1993)
• Winner, 1994 Theodore Sturgeon Award
• "The Renaissance Fair" (Sirius Visions, 1994)
• "Myths" (Andrew Vachss' Underground, 1994)
• "What Dogs Hunt in Their Dreams" (Buried Treasures, 1996)
• Dragon's Honor (with Greg Cox) (1996)
• "The Heart of a Minotaur" (The Duelist #21, January 1998)
• "The Knife's Edge" (The Duelist #23, March 1998)
• "Old Wars" (The Duelist #25, May 1998)
• "Crovax's Tale" (Rath and Storm, 1998)
• "Chenting, in the Land of the Dead" (Realms of Fantasy, November 1999)
• "The Horse Raiders" (Analog, May 2000)
• The Fox Woman (2000)
• Winner, 2001 Crawford Award
• Tales for the Long Rains (2001)
• "The Snow Wife" (Tales for the Long Rains, 2001)
• "The Knife Birds" (Tales for the Long Rains, 2001)
• "Dia Chjerman's tale" (Tales for the Long Rains, 2001)
• Fudoki (2003)
• Finalist, 2004 World Fantasy Award
• Shortlisted, 2004 James Tiptree, Jr. Award
• "At the Mouth of the River of Bees" (scifi.com; The Year's Best Fantasy and Horror 2004)
• "Elfrithe's Ghost" (Realms of Fantasy, August 2004)
• "The Empress Jing? fishes" (Conqueror Fantastic, 2004)
• "Coney World" (Coney Island Wonder Stories, 2006)
• "The Evolution of Trickster Stories Among the Dogs of North Park After the Change" (The Coyote Road: Trickster Tales, 2007; The Year's Best Fantasy and Horror, 2008; Nebula Awards Showcase, 2009)
• Finalist, 2007 Nebula Award
• Finalist, 2008 Theodore Sturgeon Award (withdrawn by Johnson, who is a juror for the award)
• Finalist, 2008 World Fantasy Award
• Final ten stories, 2008 Hugo Award
• "26 Monkeys, Also the Abyss" (Asimov's, July 2008)
• 2008 Asimov Magazine Reader's Choice
• 2008 World Fantasy Award
• Finalist, 2008 Nebula Award
• Finalist, 2009 Theodore Sturgeon Award (withdrawn by Johnson, who is a juror for the award)
• Finalist, 2009 Hugo Award
• "The Cat Who Walked a Thousand Miles" (tor.com, July 2009)
• "Spar" (Clarkesworld Magazine, October 2009)
• Winner, 2009 Nebula Award for Best Short Story
• Finalist, 2010 Hugo Award
• Finalist, 2010 Locus Award
• Finalist, 2010 Theodore Sturgeon Award (withdrawn by Johnson, who is a juror for the award)
• "Names for Water" (Asimov's, October/November 2010)
• "Ponies" (tor.com)

Other published works

• Essay, "This I Believe", aired on National Public Radio's Weekend Edition, August 31, 2008
• Essay, "Sturgeon and the Sturgeons", afterword for anthology of Sturgeon Award—winning fiction, forthcoming
• Poem, "Why She Howls: A Coyote Love Story", Journal of Mythic Arts, Winter 2006
• Comic script, "The Painted Horse", illus. Mike Dringenberg, in Dark Horse Presents, Dark Horse Comics, 1995
• Essay, "Collections: The Whole Story", Dark Horse Comics Tipsheet #4, April 1993
• Mirage: Oasis (web game for Magic: The Gathering trading card game)
• Battletech: Last Stand at Hanover (web game for Battletech trading card game)
• Weatherlight: Legacy (web game for Magic: The Gathering trading card game)
• Tempest: Into the Storm (web game for Magic: The Gathering trading card game)