This paper aims to explain the design process and systematic structure of the evaluation criteria for an “Excellent NPO,” as well as to discuss how the evaluation of a nonprofit organization (NPO) should be conducted as a measure for problem-solving. The evaluation criteria were established by the practitioners and researchers, who sensed a crisis in the current situation of the NPO sector in Japan. First, the current situation was analyzed based on the data collected, and the desirable image of an NPO was defined. Subsequently, the three problems of “citizenship,” “social innovation,” and “organization stability,” which were determined to be the most important, were extracted and defined as the basic conditions. Based on these basic conditions, the systematic structure and design process of the evaluation criteria were defined and discussions were made according to the process, thereby resulting in 33 evaluation criteria. Therefore, these evaluation criteria can help derive possible solutions for the problems faced in the NPO sector. However, in order for the evaluation to act as a problem-solving measure, the evaluation itself should be considered as a project; moreover, continuous review of the evaluation criteria, such as continuous analysis of the current situation and feedback from users, are necessary.