Rapid change and developments as well as increasing communications and dramatic developments in knowledge management, have made the existence of effective organizational performance evaluation system for the organizations inevitable. Various models have been provided by the management experts for the performance evaluation so that organizations use them according to their type of organization, mission, structure and manpower. One function of performance appraisal systems is to arouse motivation in the employees, which is addressed in this study. The present study is a descriptive-survey study. The objective of this study is to investigate the influence of employees’ performance evaluation process on their intrinsic motivation. Statistical population of this study is 80 employees of transportation organization in the Esfahan province. Research data has been collected via standard questionnaire, and SPSS software applied for the analysis. The results indicate that the process of evaluating employees’ performance affected on their intrinsic motivation (P-Value <0.05) and the effectiveness is positive, equals to 0.414.