Here's a list of first publications. Many of the stories have been reprinted. For a complete list of everything in print, check my page on the invaluable Internet Science Fiction Database.
Novels and Collections
KING OF THE DOGS, QUEEN OF THE CATS (novella) Subterranean Press, January, 2020
THE PROMISE OF SPACE (collection) Prime Books, July, 2018
MOTHER GO (novel), Audible.com, July, 2017
MASTERS OF SCIENCE FICTION: JAMES PATRICK KELLY (collection) Centipede Press, April, 2016
THE WRECK OF THE GODSPEED AND OTHER STORIES (collection) Golden Gryphon Press, October, 2008
BURN (novel) Tachyon Publications, November, 2005
STRANGE BUT NOT A STRANGER (collection) Golden Gryphon Press, September, 2002
THINK LIKE A DINOSAUR AND OTHER STORIES (collection) Golden Gryphon Press, August, 1997
WILDLIFE (novel) Tor Books, February, 1994
HEROINES, Author’s Choice Monthly (collection) Pulphouse Publishing, May, 1990
LOOK INTO THE SUN (novel) Tor Books, April, 1989 (paperback) Tor Books, February, 1990
FREEDOM BEACH by James Patrick Kelly & John Kessel (novel) Bluejay Books, October, 1985
PLANET OF WHISPERS (hardcover novel) Bluejay Books, July, 1984 (paperback) Tor Books, July, 1985
Anthologies Co-Edited with John Kessel
NEBULA AWARDS SHOWCASE Pyr Books, 2011
DIGITAL RAPTURE, THE SINGULARITY ANTHOLOGY Tachyon Publications, 2011
KAFKAESQUE, STORIES INSPIRED BY FRANZ KAFKA Tachyon Publications, 2011
THE SECRET HISTORY OF SCIENCE FICTION Tachyon Publications, 2009
REWIRED, THE POST-CYBERPUNK ANTHOLOGY Tachyon Publications, 2007
FEELING VERY STRANGE, THE SLIPSTREAM ANTHOLOGY Tachyon Publications, 2006
Short Fiction
“Your Boyfriend Experience” TWELVE TOMORROWS, Edited by Sheila Williams, M.I.T. Press (2020, scheduled)
“The Man I Love” Fantasy and Science Fiction, (March/April 2020)
“Selfless” Asimov’s Science Fiction, November-December, 2019
"Yukui!" original to THE PROMISE OF SPACE And Other Stories, Prime Books, July, 2018 and reprinted in Clarkesworld, August, 2018
"Grace’s Family” Tor.com, May, 2108
"And No Torment Shall Touch Them" Asimov’s Science Fiction, November/December, 2017
"One Sister, Two Sisters, Three" Clarkesworld, October, 2016
“Oneness: A Triptych” Fantasy and Science Fiction, July/August, 2015
“Uncanny” Asimov’s Science Fiction, September, 2014
“The Rose Witch” Clarkesworld, August, 2014
“The Chimp of the Popes” THE BOOK OF SILVERBERG, Edited by William Schafer and Gardner Dozois, May, 2014
“Someday” Asimov’s Science Fiction, April/May, 2014
“Miss Nobody Never Was” Lightspeed, December, 2013
“Sing, Pilgrim” Fantasy and Science Fiction, November, 2013
“The Promise of Space” Clarkesworld, September, 2013
“Soulcatcher” Clarkesworld, May, 2013
“The Biggest” SUPERHEROES, edited by Rich Horton, Feb, 2013
“Declaration” RIP-OFF! editedby Gardner Dozois, December, 2012
“The Last Judgment” Asimov’s Science Fiction, April-May 2012
“Bad Dogs” Escape Pod, December, 2011
“Suspicious” Daily Science Fiction, July, 2011
“Tourists” ECLIPSE FOUR: NEW SCIENCE FICTION AND FANTASY, edited by Jonathan Strahan (May 2011)
“Crazy Me” Tor.com, May, 2011
“Happy Ending 2.0” Fantasy and Science Fiction, March, 2011
“Plus or Minus” Asimov’s Science Fiction, December, 2010
“The Waiting Room” LIVE FREE OR UNDEAD, edited by Rick Broussard, November, 2010
“Going Deep” Asimov’s Science Fiction, June, 2009
“Painting The Air” Tumbarumba, January, 2009
"Surprise Party" Asimov's Science Fiction, June, 2008
"Shoppers" Nature, April, 2008
"A Small Skirmish In The Culture War" by Mike Resnick and James Patrick Kelly, THE FUTURE WE WISH WE HAD, edited by Martin H. Greenberg and Rebecca Lickiss, December, 2007
“Don’t Stop” Asimov’s Science Fiction, June, 2007
“Dividing The Sustain” THE NEW SPACE OPERA, edited by Gardner Dozois and Jonathan Strahan, May, 2007
"The Leila Torn Show" Asimov's Science Fiction, June, 2006
"Why School Busses Are Yellow" The Infinite Matrix, January, 2006
"The Edge of Nowhere" Asimov's Science Fiction, June, 2005
"Men Are Trouble" Asimov's Science Fiction, June, 2004
"The Wreck of the Godspeed" BETWEEN WORLDS, edited by Robert Silverberg, September, 2004
"The Dark Side of Town" Asimov's Science Fiction, April/May, 2004
"Serpent" Fantasy and Science Fiction, May, 2004
"The Best Christmas Ever" SciFiction, May, 2004
"Bernardo's House" Asimov's Science Fiction, June, 2003
"Mother" THE SILVER GRYPHON, edited by Gary Turner and Marty Halpern, May, 2003
"The Ice Is Singing" Realms of Fantasy, April, 2003
"Candy Art" Asimov's Science Fiction, December, 2002
"Barry Westphall Crashes The Singularity" The Infinite Matrix, September, 2002
"Luck" Asimov's Science Fiction, June, 2002
“Hubris” Realms of Fantasy, April, 2002
“The Pyramid of Amirah” Fantasy and Science Fiction March, 2002
“Unique Visitors” REDSHIFT, edited by Al Sarantonio, November, 2001
“Undone” Asimov’s Science Fiction, June 2001
"Feel the Zaz" Asimov's Science Fiction, June 2000
“Ninety Percent of Everything” by Jonathan Lethem, James Patrick Kelly and John Kessel, Fantasy & Science Fiction, September, 1999
“1016 to 1” Asimov’s Science Fiction, June 1999
“Fruitcake Theory” Asimov’s Science Fiction, December, 1998
“Bierhorst, R. G., Seera, B. L. and Jannifer, R. P. ‘Proof of the Existence of God and an Afterlife.’ Journal of Experimental Psychology. Volume 95, Spring, 2007, pages 32-36.” Asimov’s Science Fiction, August, 1998
“Lovestory” Asimov’s Science Fiction, June, 1998
“Itsy Bitsy Spider” Asimov’s Science Fiction, June, 1997
“Why the Bridge Stopped Singing” Fantasy & Science Fiction, September, 1996
“Breakaway, Backdown” Asimov’s Science Fiction, June, 1996
“The First Law of Thermodynamics” INTERSECTIONS, edited by John Kessel, Tor Books, January, 1996
“The True History of the End of the World” by Jonathan Lethem, John Kessel and James Patrick Kelly, Fantasy & Science Fiction, October/November, 1995
“Think Like A Dinosaur” Asimov’s Science Fiction, June, 1995
“Grandfather Christmas” by Robert Frazier & James Patrick Kelly Asimov’s Science Fiction, December, 1994
“Big Guy” Asimov’s Science Fiction, June, 1994
“Chemistry” Asimov’s Science Fiction, June, 1993
“Monsters” Asimov’s Science Fiction, June, 1992
“Standing in Line with Mister Jimmy” Asimov’s Science Fiction, June, 1991
“Pogrom” FIRES OF THE PAST: THIRTEEN CONTEMPORARY FANTASIES ABOUT HOME TOWNS, edited by Anne Jordan, March, 1991
“The Propagation of Light in a Vacuum” UNIVERSE 1, edited by Robert Silverberg & Karen Haber, April, 1990
“Mr. Boy” Asimov’s Science Fiction, June, 1990
“Faith” Asimov’s Science Fiction, June, 1989
“Dancing With The Chairs” Asimov’s Science Fiction, March, 1989
“Home Front” Asimov’s Science Fiction, June, 1988
“Daemon” Fantasy & Science Fiction, November, 1987
“Heroics” Asimov’s Science Fiction, November, 1987
“Glass Cloud” Asimov’s Science Fiction, June, 1987
“Rat” Fantasy & Science Fiction, June, 1986
“The Prisoner Of Chillon” Asimov’s Science Fiction, June, 1986
“Solstice” Asimov’s Science Fiction, June, 1985
“The Last” Fantasy & Science Fiction, June, 1985
“The Empty World” Asimov’s Science Fiction, November, 1984
“Crow” Asimov’s Science Fiction, September, 1984
“Freedom Beach” by John Kessel & James Patrick Kelly, Fantasy & Science Fiction, August, 1984
“Saint Theresa of the Aliens” Asimov’s Science Fiction, June, 1984
“The F&SF Diet” Fantasy & Science Fiction, March, 1984
“Friend” by James Patrick Kelly & John Kessel, Fantasy & Science Fiction, January, 1984
“Still Time” Asimov’s Science Fiction, August, 1983
“The Cruelest Month” Fantasy & Science Fiction, June, 1983
“In Memory Of” UNIVERSE 12 (Doubleday) edited by Terry Carr, April, 1982
“Identity Crisis” Twilight Zone, August, 1981
“Last Contact” Amazing, July, 1981
“Homo Neuter” ANALOG YEARBOOK II (Ace) edited by Stanley Schmidt, March, 1981
“The Fear That Men Call Courage” Fantasy & Science Fiction, September, 1980
“Flight of Fancy” Fantasy & Science Fiction, June, 1979
“Not To The Swift” Fantasy & Science Fiction, February, 1979
“Death Therapy” Fantasy & Science Fiction, July, 1978
Theatrical Plays
The Propagation of Light in a Vacuum
Breakaway, Backdown
A Swim in the Laughing Soup
I Have Not Yet Begun to Fight
The Duel
Bad Dogs
Audio Plays
“Bad Dogs” Escape Pod, December, 2011
“Carrion Death” Seeing Ear Theater, December, 2000
“Breakaway, Backdown” Seeing Ear Theater, January, 2000
"Feel the Zaz" Seeing Ear Theater, October, 1999
“The Propagation of Light in a Vacuum” Seeing Ear Theater , July, 1999
“Think Like A Dinosaur” Seeing Ear Theater, August, 199