Cogal (with Shane Dix)

• The Unknown Soldier (1995) - Re-imagined and rewritten as The Prodigal Sun

Evergence (with Shane Dix)

• The Prodigal Sun (1999)
• The Dying Light (2000) - Winner, Best Long Fiction, 2001 Ditmar Award
• The Dark Imbalance (2001) - Winner, Best Science Fiction Novel, 2001 Aurealis Award

The Books of the Change

• The Stone Mage & the Sea (2001)
• The Sky Warden & the Sun (2002)
• The Storm Weaver & the Sand (2002) - Winner, Best Fantasy Novel, 2002 Aurealis Award

Orphans (with Shane Dix)

• Echoes of Earth (2002) - Winner, Best Australian Novel, 2002 Ditmar Award
• Orphans of Earth (2003)
• Heirs of Earth (2004)

Star Wars: New Jedi Order (with Shane Dix)

• Remnant (2003)
• Refugee (2003)
• Reunion (2003)

Star Wars

• The Force Unleashed (2008)
• Fatal Alliance (2010)

The Books of the Cataclysm

• The Crooked Letter (2004) - Winner, Best Novel, 2004 Ditmar Award & Winner, Best Fantasy Novel, 2004 Aurealis Award
• The Blood Debt (2005)
• The Hanging Mountains (2005)
• The Devoured Earth (2006)

Geodesica (with Shane Dix)

• Ascent (2005) - Winner, Best Novel, 2005 Ditmar Award
• Descent (2005)

The Broken Land

• The Changeling (2008) - Shortlisted for Best Young Adult Novel, and Best Children's Novel, in the 2008 Aurealis Award.
• The Dust Devils (2008) - Shortlisted for the Best Children's Novel, in the 2008 Aurealis Award.
• The Scarecrow (2009)

Astropolis

• Saturn Returns (2007) - Winner, Best Novel, 2008 Ditmar Award

* Cenotaxis (2007) - book 1.5, novella

• Earth Ascendant (2008)
• The Grand Conjunction (2009)

Others

• Metal Fatigue (1996) - Winner, Best Science Fiction Novel, 1996 Aurealis Award
• The Resurrected Man (1998) - Winner, Best Long Fiction, 1999 Ditmar Award

• Doorways to Eternity (MirrorDanse Books, 1994)
• A View Before Dying (Ticonderoga Publications, 1998)
• New Adventures in Sci-Fi (Ticonderoga Publications, 1999) - Winner, Best Collected Work, 2000 Ditmar Award
• Light Bodies Falling (Altair Australia, 2007)
• Magic Dirt: The Best of Sean Williams (Ticonderoga Publications, 2008) - Winner, Best Collection, 2008 Aurealis Award

• "The Freezing of Sarah" (1997) in Bloodsongs #9
• "Entre les Beaux Morts en Vie (Among the Beautiful Living Dead)" (1998) in Dreaming Down-Under (ed. Jack Dann, Janeen Webb)
• "Hunting Ground" (2003) in New Australian Tales of the Supernatural (ed. Bill Congreve)
• "haikaiju" (2005) in Daikaiju! Giant Monster Tales (ed. Robert Hood, Robin Pen)
• "daihaiku" (2005) in Daikaiju! Giant Monster Tales (ed. Robert Hood, Robin Pen)
• Ghosts of the Fall
• White Christmas
• The Jackie Onassis Swamp-Buggy Concerto
• The Soap Bubble
• The Perfect Gun
• The Masque of Agamemnon (with Simon Brown)
• The Girl-Thing
• Or Die Trying (with Shane Dix)
• The Seventh Letter
• Midnight in the Cafe of the Black Madonna (Doctor Who)