Which is the relationship between mysticism and science? In order to explain that, the notion of proto-science is scrutinized within its ambivalent layers of meaning. This allows the highlighting of both the consistent and the differing features of mysticism and science. Whereas present science actually ties in with certain mystical views and performances in respect of the field of physical objects, it vehemently distinguishes itself from the mystical involvement of human consciousness and a spiritually oriented quest for God. On the one hand, this demarcation promotes the triumph of modern science accompanying the development of the contemporary self-confidence by means of experimenting in its own autonomy and methodological strength. On the other hand, it transpires that a full elimination of deeper, rationally inaccessible aspects of consciousness has been neither accomplished nor seems to be feasible at all. By means of examples, it is explained how mystical thinking and practice could be interpreted as a symbolic expression of exactly these forces of consciousness, which only enable modern scientific research in the first place. This takes place within the framework of an immanent consciousness research which is capable of uniting the holistic, existential-experiential demand of mysticism with a methodologically elaborated research concept. Such a new kind of research is ideally suited to appreciate mysticism as an immature precursor of today’s science as well as to recognize its far-reaching potentials for a trans-rational scientific culture and to implement them in a modern form.