Novels

• The Shadow Hunter (1982; partially rewritten and republished in 2002)
• The Falling Woman (1986)
• The City, Not Long After (1989)
• Nadya: The Wolf Chronicles (1996)
• There and Back Again 1999
• Wild Angel 2001
• Adventures in Time and Space with Max Merriwell 2002
• The Wild Girls 2007 (children's novel)

Collection

• Points of Departure (1990)

Anthologies

• The James Tiptree Award Anthology 1 (2005) with Debbie Notkin, Karen Joy Fowler and Jeffrey D. Smith. Anthology of winners of the James Tiptree, Jr. Award
• The James Tiptree Award Anthology 2 (2006) with Debbie Notkin, Karen Joy Fowler and Jeffrey D. Smith.
• The James Tiptree Award Anthology 3 (2007) with Debbie Notkin, Karen Joy Fowler and Jeffrey D. Smith.

Nonfiction

• Exploratopia (2006, ISBN 0316612812)
• Zap Science: A Scientific Playground in a Book (1997) by John Cassidy, Paul Doherty, & Pat Murphy
• The Science Explorer Out and About (1997) by Pat Murphy, Ellen Klages, and Linda Shore
• The Color of Nature (1996) by Pat Murphy and Paul Doherty
• The Science Explorer (1996) by Pat Murphy, Ellen Klages, and Linda Shore
• By Nature's Design (1993) by Pat Murphy
• Bending Light: An Exploratorium Toolbook (1993) by Pat Murphy
• Explorabook: A Kid's Science Museum in a Book by John Cassidy, Pat Murphy, and Paul Doherty (1991)
• "Before and After" (1997 travel essay)
• "Imaginary Friends" (1996 essay)