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Background Implementation of a mandatory insurance scheme depends on several issues, and among them are regulation, management, and program design which are very crucial. Sometimes a well-designed insurance scheme cannot attract an adequate number of people toward the scheme. Therefore, this study is aimed to explore the implementation challenges of Sajida Foundation’s health insurance scheme. Methods An exploratory qualitative research design has been applied to explore the challenges that normally exist in regular implementation process. The study population was both field and official level employees who are directly involved in the implementation process of Nirapotta scheme in Karanigoni branch. Results Successful implementation of the health insurance scheme of Sajida Foundation is getting constraints by several factors, and among them are lack of dedicated staff for this program, less involvement with community people, inadequate program knowledge dissemination to the people, and not providing incentive for work of Nirapotta are considered as the major challenges of implementation of Nirapotta Scheme. Challenges faced by policy-makers include incoordination with Microfinance Regulatory Authority and not having the latest software for perfect monitoring and evaluation of the Nirapotta program. Apart from this, there are some challenges in implementation which are normally faced in program; some of the most noteworthy findings are incoordination between employees especially in branch level, transient position of Sajida bondhu in the Nirapotta program, and low payment scale compared to other organizations. Conclusions Implementation of Nirapotta scheme is getting constraints by multiple factors which can easily be overcome by involving all necessary stakeholders and taking their valuable concern for further development of the scheme to ensure long-term sustainability of the program.