The need for systemic healthcare policies to systematically eliminate NTDs globally and in India has been stressed for more than two decades. Yet, the present policies and the research on them do not meet the need. We present an ontological framework, a research roadmap, and a policy brief to address the gap. The ontology clearly, concisely, and comprehensively represents the combinations of diseases, the objectives regarding the diseases, the entities to address them, the outcomes sought, and the potential policy instruments to invoke. The paper explicates the state of the-policies and state of the research on policies to eliminate NTDs in India. It highlights the significant gaps in the diseases covered, balance in the objectives, comprehensiveness of policies, portfolio of outcomes, and involvement of entities. Last, it presents a set of systemic policies congruent with the ontology to systematically address the gaps. The recommendations are aligned with the present research, policies, practices, and recommendations in India and of the WHO, UN agencies, and other similar bodies. The approach can be generalized to provide roadmaps for other countries facing a similar challenge and for other diseases of similar complexity. The roadmaps, with continuous feedback and learning, can help navigate the challenge efficiently and effectively.