BACKGROUND: Clinical leaders in health systems play critical roles in making decisions that impact patient care and health system performance. Current literature has focused on the importance of clinical leaders' roles in healthcare settings and has not addressed the leadership aspect that clinical leaders engage in day-to-day decision-making in HIV facilities while providing HIV patient care. Therefore, identifying the leadership roles that wclinical leaders perform at HIV primary facilities is of critical importance. PURPOSE: The study explored the views of healthcare providers working in AMPATH-MTRH HIV facility on what they perceived as the roles of clinical leaders at the HIV primary care facility. METHODS: We conducted a qualitative exploratory study between December 2019 to May 2020, involving in-depth interviews with (n = 22) healthcare providers working in AMPATH-MTRH HIV facility, who were purposively and conveniently sampled to participate in in-depth interviews to explore perceptions regarding the leadership roles of clinical leaders. The collected data were analyzed thematically and Nvivo vs.12 software was used for data management. RESULTS: The following themes were identified from the analysis regarding perceived clinical leaders' roles in an HIV primary care facility: 1) Strategic roles: providing direction and guidance, ensuring goals and objectives of the department are achieved within the set timelines, planning, and budgeting for adequate resources to support patient HIV care 2) Interconnecting health systems levels and supervisory oversight roles: a link between management, staff, and patients, solving problems, organizing and attending departmental meetings, facilitate staff training, accountable, collaborating with other departments and leaders, defines and assigns responsibilities, ensure quality patient service, coordination, and management of daily activities 3) Research roles: data collation, analysis, generation, review and reporting to the management. CONCLUSION: Clinical leaders in the HIV care system perform leadership roles that are characterized by strategic, middle-level, supervisorial and research which reflects the model of the leadership and management style of the HIV care system. The understanding of these roles contributes valuable insights to HIV leaders and managers to recognize the important contribution of clinical leaders and consider reviewing Standard Operating Procedures to include these leadership roles and strengthen their capacity to maximize clinicians' contribution to improve HIV care and enhance responsive health systems.