Rare diseases (RD) are conditions that affect a small number of people and hence do not get the focus on government health priorities in a resource-constrained setting such as India. The National Health Mission (NHM) is one of the crucial programs initiated by the government of India to address the health needs of the under-served. NHM programs can provide a unique epidemiological data repository to strengthen the National Rare Disease Registry. These programs can also play important role in providing a continuum of care for many RDs that need lifelong management. However, existing programs have a limited scope to provide specialized RD-related treatments, which is better served in a more focused system. Thus, considering RDs in the design of the existing programs may help RD management better through prevention, data collection, and providing a continuum of care.