Background and Objective: Assessment and evaluation of quality of education and performance of academic departments at universities are highly important. A common model to evaluate performance of an organization and its branches is Balanced Score Card. This study aimed to develop a model based on Balanced Score Card and Analytic Hierarchical Process in order to assess the performance of academic departments of Zanjan School of Pharmacy.

Materials and Methods: In this descriptive study, 24 academic members of six departments of Zanjan Pharmacy School and 100 pharmacy students were surveyed. Data was gathered through questionnaires and semi-structured interviews. Collected data was organized by Excel and then weighted and analyzed using Expert Choice software version11 and SPSS 16.

Results: According to results, in the learning environment, growth and development dimension with weighted score of 0.377, customer (0.345), process (0.158) and financial perspective (0.121) were ranked respectively. Pharmaceutics and food and drug control departments achieved highest performance respectively.

Conclusion: Findings of this research could be used to provide and develop an appropriate combination of BSC and AHP techniques to give an image of four perspectives application of BSC in educational environment and in addition it can be used in planning and promoting the performance of similar educational systems by improving the quality of performance assessment and ranking.