The COVID-19 pandemic has indirectly changed the landscape of the country’s education system. Through information-based decision-making, the management of the education system seeks to increase the access to and efficiency, effectiveness, equity and quality of education through effective systems of monitoring, evaluation, budgeting and planning. From this perspective, an Integrated National Education Information System (iNEISTM) was developed to streamline and transform business processes and to provide an application and technology platform to comply with the National Education System that may be suitable for the COVID-19 pandemic environment. The implementation of iNEIS™ aimed to significantly improve operational efficiency and productivity and provide better services, value and “holistic education” to students. Therefore, the purpose of this study was to investigate the effectiveness of the newly implemented, integrated iNEISTM and its implications for educational management systems that were implemented during the COVID-19 pandemic. It specifically examines the benefits and obstacles that hinder the efficiency and effectiveness of the system. The result is very interesting. These findings demonstrate that there was a lack of positive impact on end-users, such as lacking readiness to accept organizational change and uncoordinated communication and information exchange between stakeholders and end-users. This research implies that when both the stakeholder-provider and end-user understand the significance of iNEISTM, there is a great possibility that the implementation will succeed in harvesting the full value of the system. This paper provides the stakeholder-provider with useful guidelines, in the form of recommendations, that need to be implemented to ensure improvement in the effectiveness of iNEISTM.