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)
See also Pataphysics
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.
Along with Lisa Goldstein and Michaela Roessner, she has formed The Brazen Hussies to promote their work.kool
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)