Introduction. Most current theoretical explanations of “how polygraph testing works” are done within the framework of an outdated stimulus-reactive paradigm. This article attempts to analyse the manifestations of this paradigm in the phenomena within the problematic field of polygraph-based research. Methods. The study employed the following methods: analysis of scientific and methodological literature; analysis of regulatory, legal, and methodological documents governing the conduct of polygraph examinations; and analysis of activity products – namely, expert reports based on the results of polygraph examinations. Results. The theory and practice of polygraph examinations face several key challenges: the issue of the “psychophysiological phenomenon”; the issue of the correlation between a psychological stimulus and a physiological response; the issue of determining the “significance” of a stimulus; the issue of the phenomenology of “memory traces”; and the issue of the scientific incorrectness of expert conclusions based on polygraph examination results, among others. The analysis suggests that these problems are a consequence of the predominance of the stimulus-reactive paradigm in the theoretical justification and practical application of the “polygraph method”. This paradigm rejects the primacy of internal determinants of human activity over external ones and ignores modern achievements in sciences such as psychology and psychophysiology. This paper argues that polygraph examination, as a form of instrumental psychological experiment, must develop its theoretical and methodological foundations in accordance with modern scientific perspectives on human activity within natural life contexts.