Digital entrepreneurship is an essential driver within the innovation system. It changes the structure, aims, and networking mechanisms of the overall business system and, ultimately, affects the various levels and dimensions of the innovation system. Bringing inevitable changes to the innovation system, digital technologies may not only provide new business opportunities but also be disruptive and cause new vulnerabilities. In order to gain a rigorous understanding of the hybrid concept of digital entrepreneurship and its role within the transformation of the innovation system, we conducted a systematic literature review. The results of 52 core papers allow for the identification of key categories of digital entrepreneurship and also its differentiation from other types of business activities. The analysis leads to the distinction of the determinants of digital entrepreneurship within three core dimensions of the innovation system, which encompass the entrepreneur (including, e.g., behavioral, competence. and mentality patterns, as well as personal outcomes and consequences of entrepreneurial activity), the entrepreneurial process (including activities that concern digitalization in organizational management processes, transformations within strategic and operational activities, and digital start-up establishment), and its relevant ecosystem (which encompasses, among others, the influence that external infrastructure and institutions have on digital entrepreneurship development). The systematization of the existing literature is highly relevant for future research that aims to understand the interrelations between the transformation of entrepreneurial structures within innovation systems as well as the socioeconomic system in general. Such understanding requires further extended research in fields related to method, content, and theory.