Operators of rural tourism face various difficulties that hamper development of their activities. This paper explored the roles that NPOs play in the development of rural tourism to help operators counter such difficulties. For this purpose, the author firstly presented a conceptual framework from the perspective of institutional economics that explains why development of a rural tourism activity is often slow. It was revealed that the high marginal cost of acquiring skills in local resource management should be reduced to counter that slow development. Secondly, the author empirically evaluated the significance of NPOs through a case study in Chiba, Japan, that works to horizontally integrate stakeholders. This type of NPO provides services to ease difficulties encountered by operators by network building among stakeholders, providing training opportunities, negotiating with travel agencies, and assisting in program development in which many other stakeholders are not always proficient. This type of NPO can reduce the marginal cost of local resource management, which eventually leads to the development of rural tourism. Thus, it is expected that roles of this type of NPO will increase in the future. Partnerships with NPOs will be important in the design of policy measures for rural tourism.