Main objective of the present survey is to conduct a comparative analysis of the challenges of the performance evaluation system in two private and public sectors and their impact on effectiveness of human resources management practices. This survey was conducted using the field-descriptive method. The historical study method was used to collect theoretical subjects and the field study method was applied to answer the research questions and confirm or reject the research hypotheses. Statistical population of the research included all experts and managers at various levels in two private and public sectors of the petrochemical industry. Cluster-stratified sampling method in two phases was utilized. According to the results of the present survey, there is a significant difference among identified challenges in the performance evaluation system in two private and public sectors of the petrochemical industry. Results demonstrate that the effectiveness level of human resource management practices in the performance evaluation system is higher than the average level in the public sector, effectiveness level of human resource management practices in the performance evaluation system is lower than the average level in the private sector of the petrochemical industry, and there is a significant difference between the effectiveness level of human resource management practices in the performance evaluation system in two private and public sectors of petrochemical industry. Studying the impact of existing challenges in the performance evaluation system on effectiveness of human resource management practices shows existence of a significant and reversed relation among the existing challenges in the performance evaluation system and effectiveness of human resource management practices in this regard.