The objectives of the study are to explore the perception of Microfinance Institutes (MFIs) on Social Entrepreneurship (SE) and to examine the application of Positive Theory of Social Entrepreneurship (PTSE) in the MFIs in Sri Lanka and to identify unique social entrepreneurial characteristics in MFIs in Sri Lanka. This is a qualitative study carried out through primary data collected mainly from in-depth semi-structured interviews with 5 Chief Executive Officers (CEOs) representing 5 microfinance institutes in Sri Lanka who owned the largest microfinance loan portfolios. For the data analysis purpose thematic analysis method was used in the study. MFIs perceived the concept of social entrepreneurship as a social obligation parallel with profit making or as the obligation of the organization towards the society while achieving their commercial objectives. Application of the PTSE in the selected MFIs in Sri Lanka showed that four propositions on SE proposed in the theory can be observed to a considerable extent in the MFIs in Sri Lanka. Unique social entrepreneurial characteristics identified in the MFIs in Sri Lanka were adherence to the deep rooted values of MFIs, much flexible approach when dealing with microfinance clients, impact from other stakeholders on MFI to perform social entrepreneurial role, and the co-operative model of MFIs tended to promote SE.