The aim of this paper is to present a systematic reconstruction of the development of the pansophic idea in the work of Jan Amos Comenius. The concept of pansophia, rooted already in the ancient philosophical thinking, became a very popular topic of sixteenth- and seventeenth-century discussions, and it is one of the central topics of Comenius’s philosophy. It is assumed that Comenius elaborated the formulation of the pansophic program—i.e., the program for creating a universal science incorporating the findings of both the profane and the divine—at the end of 1630s. This study therefore aims to analyse all relevant Comenius’s treatises and attempts to identify the individual development phases of Comenius’s pansophic idea until its transformation into the idea of the universal reform, panorthosia. The analysis of Comenius’s treatises is complemented with a reflection on Comenius’s correspondence, which facilitates the understanding of the author’s more private motives.