Gee graduated from BYU in 1988. Later, he became a graduate student in Near Eastern Studies at the University of California, Berkeley and received his M.A. in Near Eastern Studies in 1991. He earned his Ph.D. in Egyptology at Yale University in 1998, completing his dissertation on ancient Egyptian ritual purity.

Gee is the William "Bill" Gay Associate Research Professor of Egyptology at the Neal A. Maxwell Institute for Religious Scholarship at BYU. In this role, he is an editor for the Studies in the Book of Abraham series and a member of the editorial board of the Eastern Christian Texts series.

Gee has been involved with various professional societies. He is editor of the Journal of the Society for the Study of Egyptian Antiquities, and has served on the Society's committees and board of trustees. He was also on the board of directors for the Aziz S. Atiya Fund for Coptic Studies at the University of Utah. He has participated in the International Association for Coptic Studies, the Society of Biblical Literature, the American Research Center in Egypt, and the David M. Kennedy Center for International Studies.

Gee has written an overview of Coptic literature. In May 2008 Gee gave a presentation on the early conversion to Christianity in Egypt at the Coptic Church Center in London.

Gee is a believing member of The Church of Jesus Christ of Latter-day Saints (LDS Church), which believes Joseph Smith divinely translated the Book of Abraham from Egyptian papyrus in the 19th century. Because of his expertise in Near Eastern studies and Egyptology, Gee is highly visible in the debate over the authenticity of the Book of Abraham. His interest in these issues led to his involvement with the Foundation for Ancient Research and Mormon Studies (FARMS) at BYU since the late 1980s. He has also presented on the Joseph Smith Papyri to the Foundation for Apologetic Information & Research (FAIR).

One of Gee's former Yale professors, Robert K. Ritner, later publicly criticized some of Gee's interpretations of the Joseph Smith Papyri and failure to include Ritner in professional peer reviews of his work, as his other students have.

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