The relevance of Management Control System (MCS), Good University Governance (GUG) and internal auditor’s role has become crucial in realising excellent service of the university to the community. The effectiveness of the role and relationship of these three factors, particularly in the State University is still limited and relatively partial, whereas the measurement is not broad and not in the alignment system model (fit model). The objective of this study is to prove the role of MCS on GUG with the internal auditor’s role as a mediation. Results of the test by using structural equation modelling (SEM) showed that the indicators of each variable valid and reliable. This study proves that the effectiveness of MCS affects the GUG, but the internal auditor’s role is not significant. Thus, this study does not support the effectiveness of the MCS role in the achievement of GUG through internal auditor’s role. Auditors are still influenced by the old paradigm that is as a watchdog, the representative of the Chairman and not as a catalysator. However, this study confirms the indicators of the effectiveness of MCS, GUG and the role of internal auditors. Based on the findings, the competency of the internal auditors should be improved, especially in time management, communication skills, searching for evidence and explaining recommendations. The results of this research would be more interesting for further study if it were to be re-examined in the context of higher education with different characteristics and ownership status.