As a child, Thompson was home-schooled at the Lindisfarne Association, a thinktank and retreat founded by his father, William Irwin Thompson. In 1977, Thompson met Chilean phenomenologist Francisco Varela when Varela attended a Lindisfarne conference which was organized by Thompson and Gregory Bateson. Thompson received a Ph.D. in Philosophy from the University of Toronto in 1990 and an A.B. in Asian Studies from Amherst College in 1983.
Thompson has taught at the University of Toronto, Concordia University, Boston University, and York University. While at York University, Thompson was also a member of the Centre for Vision Research. Thompson has held visiting appointments at the Center for Subjectivity Research in Copenhagen, and at the University of Colorado, Boulder. Thompson worked with Francisco Varela at CREA (Centre de Recherche en Epistemologie Appliquée) at the Ecole Polytechnique in Paris. During this time, Varela and Thompson wrote The Embodied Mind: Cognitive Science and Human Experience. Thompson's latest book, Mind in Life: Biology, Phenomenology, and the Sciences of Mind, explores how life relates to mind.
- Francisco Varela, Evan Thompson, and Eleanor Rosch, The Embodied Mind: Cognitive Science and Human Experience. MIT Press, 1991.
- Colour Vision: A Study in Cognitive Science and the Philosophy of Perception Routledge Press, 1995
- Between Ourselves: Second Person Issues in the Study of Consciousness. Imprint Academic, 2001. Published also as a special triple issue of the Journal of Consciousness Studies
- Alva Noe and Evan Thompson, eds., Vision and Mind: Selected Readings in the Philosophy of Perception. MIT Press, 2002.
- The Problem of Consciousness: New Essays in Phenomenological Philosophy of Mind. Canadian Journal of Philosophy, Supplementary Volume 29: 2003. University of Alberta Press
- Giovanna Colombetti and Evan Thompson, eds., Emotion Experience. Imprint Academic, 2005. Published also as a special triple issue of the Journal of Consciousness Studies
- The Cambridge Handbook of Consciousness Edited by Philip David Zelazo, Morris Moscovitch, Evan Thompson May 2007 Cambridge University Press Cambridge Handbooks in Psychology series (ISBN 9780521674126)
- Mind in Life: Biology, Phenomenology, and the Sciences of Mind Harvard University Press