Trypanosoma and Leishmania species are responsible of a range of Neglected Tropical Diseases (NTDs) from disfiguring conditions to fatal processes in humans. Both genera also affect wild and domestic animals causing diseases of public health significance and high economic impact on farm economy of developing areas. Japan has been actively involved in overseas cooperation and the country has a large scientific community. However, there is no information on the scientific output of Japanese scientists and institutions on these two NTDs. To explore the Japanese contribution and its profile, we have mined Web of Science database from 1971 to 2022 the articles by Japanese scientists, scientific areas and institutions, time-related variations of these parameters, and involvement in cooperation activities with foreign scientists. Research on Trypanosoma has been present in all the studied period, with higher production, whereas Leishmania-related activities showed a delay. A steady increased of Japanese scientific output was found up to the beginning of 2000s, whereas a certain stagnation was found in the present century. Low growth rate of research output on these two NTDs by Japanese authors in the 21st century is not correlated neither to the pattern found globally nor the situation in other parasitic infections. Thus, other elements should be considered in future analysis including the actual number of scientists involved and the available funding. Reinforcement of research groups from Japanese institutions and widening the scope of collaborations, particularly with health and academic centers from endemic regions, could trigger the Japanese productivity in the research area.