BackgroundAn effective health headquarter worker has behaviors, knowledge, skills, and motivations which are behavioral, technical, and motivational prerequisites for successful performance in a job. This study aims to identify the general competencies of health headquarters workers to meet the needs of the health system.MethodsWe used multiple qualitative methods to facilitate a consensus-building process on developing core competencies. First, we used systematic review and meta-synthesis to identify the dimensions and components of core competencies. Using a critical case sampling, we interviewed twenty-six participants and analyzed the information with thematic content analysis. In the third phase, we divided the health headquarters workers into three levels. Then, to present the initial model of competencies, the Mini Delphi method was used. Finally, in the fourth phase, to reach a consensus on the importance of each competency and determine the level of competencies required for each level of health headquarters workers, three-step Delphi method was used, and we presented the final model.ResultsWe presented a competency model for three levels of health headquarters workers. The main competencies are (1) leadership and management (12 components), (2) analysis, interpretation, and reporting (6 components), (3) interpersonal relationships (4 components), (4) individual competencies (7 components), (5) cultural and community competencies (5 components), (6), and administrative competencies (4 components). All competencies are needed for the third level of health headquarters workers. In general, second and third levels of health headquarters workers need high and middle level of required competencies that mean these workers' levels should have all competencies before using them in top of national health organizations. ConclusionThe competencies were extracted due to the levels of health headquarters workers, as well as the level of competencies required by each group of experts, could act as a guide for policy-makers and managers related to human health resources in the health sector, and help them adopt appropriate strategies to employ and train health headquarters workers.