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

THE PROMISE OF SPACE (collection) Prime Books, (not yet scheduled)

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 (hardcover 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 ANTHOLOGYTachyon Publications, 2011

KAFKAESQUE, STORIES INSPIRED BY FRANZ KAFKA Tachyon Publications, 2011

THE SECRET HISTORY OF SCIENCE FICTIONTachyon Publications, 2009

REWIRED, THE POST-CYBERPUNK ANTHOLOGY ( Tachyon Publications, 2007

FEELING VERY STRANGE, THE SLIPSTREAM ANTHOLOGYTachyon Publications, 2006

Short Fiction

“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