Thisse is Professor Emeritus of Economics and Regional Science at the Catholic University of Louvain and at the École des Ponts ParisTech.

In a 2020 interview to the European Regional Science Association (ERSA), Thisse said that the main question that had sparked his interest was "What could be the economic justification for the existence of cities?

He was director of CERAS, Ecole Nationale des Ponts et Chaussées (Paris) from 1992 to 1996 and president of the Center for Operations Research and Econometrics, UCLouvain, from 2000 to 2006.

Thisse’s research in industrial organization was synthesized and extended in Discrete Choice Theory of Product Differentiation, a book co-authored with Simon P. Anderson and André de Palma and published by MIT Press in 1992.

His work explores how cities organize themselves based on the interactions between these economic factors, with a special emphasis on environment, metropolitan areas, and market integration.

Thisse's research often involves quantitative spatial models and stylized geographies, aiming to provide a comprehensive analytical characterization of urban equilibrium and stability across various parameter spaces.