Background and Objectives: Assessment, identification, and presentation of management challenges of running programs can help policymakers and administrators to overcome these deficiencies and achieve the objectives of the plan. This study was conducted with the aim of explanation of the management challenges and solutions for its elimination in the health sector of health system reform plan Qom city. Methods: In this qualitative study, participants were the experts and the executives of Qom health center, health services providers in the health centers affiliated to the deputy of health of Qom University of Medical Sciences and health services recipients referring to health centers in Qom city, selected by convenience sampling. The data were collected through individual interviews using a semi-structured questionnaire and analyzed by qualitative content analysis and an inductive approach. Challenges for health system reform in the field of health, were extracted by qualitative method. Results: The data of this study were categorized in 21 categories and 7 themes. From the perspective of the participants, the management challenges of health system reform in the health sector included waste of resource, the unexceptionable system, hasty implementation of the program, emphasis on quantity and directional reporting, ineffective monitoring, shortcomings in implementation of the program, and reduced quality of health services. Conclusion: Based on the findings of this study, it is necessary to design effective strategies for management of resources, establishment of a system for collecting criticisms and suggestions and their application, judgment based on the quality of services, modification of the existing monitoring system, eliminating executive failures, and paying attention to the improvement of the quality of services.