Fundamental benefits suggest that biomedical engineering and medicine should form a more convergent alliance, especially for the training of tomorrow’s physicians and biomedical engineers. Herein, we review the rationale underlying these benefits. Biological discovery has advanced beyond the era of molecular biology into the new, still largely uncharted era of molecular systems biology. The concomitant shift in focus toward understanding the fundamental rules and principles governing the behavior of complex living systems has important medical implications. To realize cost-effective personalized medicine, it is necessary to propagate the emerging advances in molecular systems biology to higher levels of biological organization that focus on organs, organ system, and whole organisms, and then to develop new, individualized medical therapeutics based on medical informatics and targeted computer simulations. To accomplish these goals, higher education in the biological and medical sciences must adapt to new training objectives. This adaptation must involve a shifting away from reductionist problem solving toward more integrative, systemic, and predictive modeling approaches that traditionally have been more associated with education in engineering. Future biomedical engineers and MDs must be able to predict clinical responses to therapeutic interventions. This necessity mandates that medical training must become more like engineering education, wherein future physicians are taught fundamental rules governing complex system behaviors and skill sets for manipulating these systems to achieve practically feasible, desired clinical outcomes. Correspondingly, graduate biomedical engineering programs must increase the students’ practical exposure to pressing clinical problems. The fundamental goal of medical intervention is to accomplish a sustained beneficial change in the behavior of a complex feedback-controlled homeostatic system (i.e., the patient). The direct and indirect responses of such systems to any substantial interventions are notoriously difficult to fathom by the unaided human mind, thus begging the question how modern science and engineering may help. There appears to be great potential for medical students to gain benefits from learning and engaging in models of engineering control systems applied to medical practice. A particularly powerful target domain is regenerative medicine, which is already accustomed to translating engineering concepts into medical advances. Tissue engineering, organoid development, and regenerative medicine are prime examples of promising new technologies that will ultimately require a grasp of fundamental bioengineering control theory, not simply for understanding how biological systems work, but also for envisioning how we can exert steady-state control in these living, adaptive systems. Here, we propose that near-future medical education should shift toward integrative analysis of system function and malfunction and toward the development of therapies utilizing control concepts. Such a shift will eventually make personalized medicine feasible, practical, and affordable, but requires a significant rethinking of existing pedagogical tools.