Recently, mathematical models based on quantum formalism have been developed in cognitive science. The target articles in this special issue of Topics in Cognitive Science clearly illustrate how quantum theoretical formalism can account for various aspects of human judgment and decision making in a quantitatively and mathematically rigorous manner. In this commentary, we show how future studies in quantum cognition and decision making should be developed to establish theoretical foundations based on physical theory, by introducing Taketani's three-stage theory of the development of science. Also, implications for neuroeconomics (another rapidly evolving approach to human judgment and decision making) are discussed.