In today's competitive environment, business, the success of business entities depends on the continuous improvement process. This is conducted through goal setting, planning and implementing programs and thus performance evaluation. In the past, performance evaluation was carried out relying only on financial measures. Financial measures that reveal the historical events were sufficient for evaluating the performance of companies in the industrial age, in which a long-term capabilities and customer relationships were not considered as vital factors in achieving success. However, these criteria are not enough for conducting and evaluating the performance of companies in the current era, in which the creation of value and wealth promotion is possible through investment in customers, suppliers and users of material goods, personnel, processes, technology and innovation possible. In addition to financial measures, Balanced Scorecard provides new measures to adapt the methods of assessments to the present situation. Experience shows that the implementation of this system has faced challenges that the present study is to investigate them. The present research is of applied-descriptive type. The population consists of people in charge of the enforcement and implementation of the Balanced Scorecard professionals, accountants and management accounting and management professors and universities are institutions of higher education. To collect data, 240 questionnaires were sent during the first quarter of 1391. The results of this study showed that the country's political and economic fluctuations, successive changes in strategies, unfamiliarity of managers with the concept and the advantages and how to implement the Balanced Scorecard and to determine performance indicators and standards are the main obstacles to the implementation of the system in Iranian companies.