Aims: Universities and other higher education institutes play critical role in the development of the knowledge-oriented social. Intellectual capital is the main element in achieving the stable competitive advantage. This study was conducted aiming at examining the role and relationship between intellectual capital and the performance of university system.

Methods: This study was a survey which was conducted in 2002 in the 6 universities of Iran, and two sample groups were included in the study. Research instrument consisted of two university expert researcher-made questionnaires and the intellectual capital condition poll in universities. For data analysis, Pearson correlation test, stepwise regression, single-sample T-test and multivariable variance analysis (ANOVA) were used and analysed in SPSS 13 statistical software.

Results: University system performance mean was 52.87±36.30 in faculty members’ opinion and had significant and positive relationship with human capital, relationship capital, and structural capital. There was a significant relationship between academic system performance and subcomponent of faculty members, student, personnel, cultural organization, relationship with industry, and scientific interactions. There was significant difference between the human capital component and relational capital between universities. However there was no significant relationship between structural capitals between universities.

Conclusion: Intellectual capital components have influence on the academic system performance. Moreover, In accordance with the average condition of Iran universities in these components, more desirable management of the intellectual capital in the universities and higher education institutes causes academic system performance improvement.