This paper analyses the role of political economy to influence innovative behavior of social entrepreneurs. The paper consists of critique on the understanding and interpretation of social entrepreneurship from the perspective of political economy. Review of past studies reveals limited analysis on the role of political economy in mediating the innovating behavior and functions of social entrepreneurs. In this study while dragging the theoretical perspective in analyzing the practical experience, opinion of some selected social entrepreneurs in Nepal have been collected and analyzed. Findings are based on the analysis of thematic and content analysis of the past studies and the opinion collected from the interviews of social entrepreneurs. The main aim of the paper is to get insight into the role of political economy in influencing innovative behavior of social entrepreneurs. The approaches and methodology applied include review of theories on political economy and its interconnection between the innovation and social entrepreneurship. Method applied to achieve objective covers content and thematic analysis of the interviews of selected Nepali social entrepreneurs. Theories relating to the each of the thematic areas have been reviewed from the literature available in books, journals, newspaper, magazines and different internet sources. It is seen that innovation is independent work of an individual which generally happens to be indifferent with the political, economic and social system but a good system of political economy can influence the innovative behavior and can play a significant role to flourish social entrepreneurship more effectively.