Background: There is a high burden of morbidity due to neglected tropical diseases. To help address this, the World Health Organization recommends integration of case management (CM). Here, we present a practical framework designed to identify areas that could benefit from an integrated CM strategy in Ghana. We also investigated the accessibility of primary health care (PHC) to CM cases, and the impact of this on morbidity at diagnosis. Methods: Routinely detected cases of Buruli ulcer (BU) and leprosy, and suspected lymphedema identified through morbidity surveys during mass drug administration campaigns in Ghana in 2014 were remotely georeferenced. We estimated distances from cases’ home communities to the nearest primary healthcare facility (PHC), and compared rates of reported disease, completeness of clinical information, and risk of more severe morbidity, relative to PHC accessibility. Results: We georeferenced communities of 295/350 reported leprosy cases, 240/333 BU cases, and 1,557/2383 instances of lymphedema. Overlap of these diseases was predominantly around Accra and in the Upper East Region. Rates of reported disease appeared higher in populations with higher accessibility to PHC, and leprosy cases living further from PHC had a higher risk of disability at diagnosis. Conclusions: This investigation demonstrates the feasibility and value of using routinely collected data to map CM-NTDs at low cost. The maps presented are intended to provide a resource for planning the implementation of integrated CM for NTDs in Ghana. This approach could be easily implemented by national health services in other endemic countries in the future.