Thornton received his B.S. from St. Bonaventure University (1982), and his Ph.D. from Auburn University (1989). Thornton taught economics at Auburn University for a number of years, additionally serving as founding faculty advisor for the Auburn University Libertarians. He also served on the faculty of Columbus State University, and is now a senior fellow and resident faculty member at the Ludwig von Mises Institute. He is currently the Book Review Editor for the Quarterly Journal of Austrian Economics.

Prohibition studies

Libertarian organizations including the Independent Institute, the Cato Institute, and the Mises Institute have published Thornton's writings on drug prohibition and prohibition in general. He has also been interviewed on the topic of prohibition by members of the mainstream press. Thornton's first book, The Economics of Prohibition, was praised by Murray Rothbard, who declared:

Thornton's book... arrives to fill an enormous gap, and it does so splendidly.... The drug prohibition question is... the hottest political topic today, and for the foreseeable future.... This is an excellent work making an important contribution to scholarship as well as to the public policy debate.

Economic bubbles

Thornton has also written on economic bubbles, including the United States housing bubble, which he first described in February 2004. He suggested that the "housing bubble might be coming to an end" in August 2005. His work on market bubbles has been cited by journalists and other writers. Joseph Salerno said, "Mark Thornton of the Mises Institute was one of the first to jump on this...to start writing about the housing bubble."

Thornton has also been active in the political arena, making his first bid for office in 1984, when he ran for the U.S. Congress. He became the first Libertarian Party office-holder in Alabama when he was elected Constable in 1988. In addition to further political candidacies, Thornton also served in various capacities with the Libertarian Party of Alabama. In 1996 he became an economic advisor to Alabama Governor, Fob James.

Thornton has been featured as a guest on a variety of radio and internet programs and his editorials and interviews have appeared in leading newspapers and magazines.