Abstract: E-learning in its various forms is the future of flexible and effective learning that takes advantage of the capabilities of the contemporary technological revolution. At a time when universities are increasingly using the blended learning model, this study aimed to provide an insight into the management information systems that support the blended learning process in universities. As evidenced by its name, the Egyptian University for E-Learning (EELU) was born as an electronic university, so, it did not need digital transformation like other universities that started with the traditional learning system. EELU adopted the blended learning model that combines part of the study that takes place face to face and the other part using E-learning technologies such as virtual classrooms and the like. The main objective of this paper is to shed light on management information systems in universities that adopt the blended learning model and to take a closer look at both the learning management system and the university management system through a case study of EELU where the use of those systems in the university was monitored over a period of approximately five Years and define the challenges they face. Through EELU case study, the paper shows that the learning management system and the university information system work independently, there is some compatibility between the two systems that can be described as a partial compatibility regarding the exchange of data between one system and another. The paper recommended a step-by-step approach in implementing the information systems integration strategy within the university.