The paper substantiates the relevance of developing the concept of managing stakeholders in the educational agglomeration based on the flexible methodology in an unstable environment. The aim of the paper is to conceptualize the management of stakeholders of educational agglomeration based on the Agile methodology. The main research methods were dialectical method, critical analysis method, descriptive statistics methods, communicative and pragmatic approach, stakeholder approach, and conceptualization. The concept of managing stakeholders in the Russian educational agglomeration based on the Agile methodology was developed. This conceptualization implements the empirically-based and design-based orientation of the flexible methodology and takes into account the practical benefits of stakeholder effects from participation in the educational agglomeration. The main elements of the stakeholder management system are: the person, object and subject of management, management principles, management cycle and management of the terms of cooperation. The conclusion about managing the stakeholders of the educational agglomeration based on the Agile methodology is substantiated.
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