The present study explores the relationship between the systemic approach, educational innovation, and the use of digital technologies in higher education, with an emphasis on military academies. The aim of the research is to shed light on how systemic thinking can support strategic planning, the quality of education, and the effective integration of innovative practices, such as artificial intelligence, information and communication technologies, and virtual reality. The methodology was based on quantitative research using a questionnaire, which was distributed to 452 members of the Hellenic Non-Commissioned Officers Academy educational community (teaching staff, cadets, and recent graduates). Data analysis showed that the adoption of a systemic approach is positively associated with the readiness of trainers, including both instructors and future professionals (cadets), to support and implement educational innovations. Furthermore, it was found that the clarity of educational objectives and the alignment of critical elements of the educational system (resources, technology, instructors, trainees, and processes) significantly reinforce the intention to adopt innovative practices. The findings also show that educators’ positive perceptions of artificial intelligence and virtual/augmented reality are associated with a higher appreciation of learning benefits, such as improved performance, trainee satisfaction, and collaboration. In contrast, demographic and professional factors have a limited effect on attitudes toward innovation. Overall, findings indicated that innovation in military academies is not limited to the technological dimension, but requires a holistic, systemic approach that integrates organizational, pedagogical, and strategic parameters. The study contributes both theoretically and practically, providing empirical evidence for the role of systemic thinking in the design and implementation of innovative educational policies in military and broader academic education.