In this study we aimed to explore how managers in primary health care (PHC) organizations assess their managerial knowledge and skills, as well as the importance of these competencies for their job, and to identify whether there is an alignment between these two perceptions; therefore, whether there is a need for management competency improvement. With this study, we tried to address a high demand for information about health managers, especially in health systems in low- and middle-income countries. In a sample of 58 primary health care centers (n = 106 managers) in Serbia, we used a basic managerial competency matrix consisting of the following six competencies—communication, team-building, planning and priority-setting, performance assessment, problem-solving, and leading. Managerial perception of the importance of their job tasks differs by educational level and managerial position. The best alignment between the importance of knowledge and skills was for communication and leading. The study pointed out that managers were aware of the necessity to improve their level of managerial competencies, particularly in the domains of planning and priority-setting, performance assessment, and problem solving. The study highlights the need for formal managerial education for managers in PHC settings and commitment to continuously evaluate and improve management competencies in order to better manage PHC.