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Background “Contracting Out” is a popular strategy to expand coverage and utilization of health services. Bangladesh began contracting out primary healthcare services to NGOs in urban areas through the Urban Primary Health Care Project (UPHCP) in 1998. Over the three phases of this project, retention of trained and skilled human resources, especially doctors, proved to be an intractable challenge. This paper highlights the issues influencing doctor’s retention both in managerial as well as service provision level in the contracted-out setting. Methodology In this qualitative study, 42 Key Informant Interviews were undertaken with individuals involved with UPHCP in various levels including relevant ministries, project personnel representing the City Corporations and municipalities, NGO managers and doctors. Verbatim transcripts were coded in ATLAS.ti and analyzed using the thematic analysis. Document review was done for data triangulation. Results The most cited problem was a low salary structure in contrast to public sector pay scale followed by a dearth of other financial incentives such as performance-based incentives, provident funds and gratuities. Lack of career ladder, for those in both managerial and service delivery roles, was also identified as a factor hindering staff retention. Other disincentives included inadequate opportunities for training to improve clinical skills, ineffective staffing arrangements, security issues during night shifts, abuse from community members in the context of critical patient management, and lack of job security after project completion. Conclusions An adequate, efficient and dedicated health workforce is a pre-requisite for quality service provision and patient utilization of these services. Improved career development opportunities, the provision of salaries and incentives, and a safer working environment are necessary actions to retain and motivate those serving in managerial and service delivery positions in contracting out arrangements.