This study aimed to examine the practice of Educational Management Information Systems in Oromia and to identify the major challenges which are hindering its effectiveness. A qualitative case study research design was used to address the aim of the study. Data were collected from both primary and secondary sources through focus group discussions with 8 well-experienced individuals from ICT and EMIS directorate and reviewing the regional education statistics annual abstracts published within the last five years. Thematic data analysis was used to analyze the data obtained from both sources. The findings of this study revealed that the practice of EMIS in the region is characterized by time-consuming, paper-based work and tiresome. Meanwhile, it was found that there are challenges like skill and knowledge gaps among people having different functions in the system, poor organizational structure and absence of EMIS policy and legal framework as well as absence and inadequate availability of hardware, software, internet connectivity and electrical power, especially at schools level and remotest areas of the region. It was concluded that although the system is characterized by poor data quality, it can be considered as effective for it is delivering the required education data and information needed by different stakeholders. It was recommended that most of the challenges can be improved if officials at different levels pay due attention to the issues. It was also recommended that further research needs to be conducted to come up with appropriate interventions for the challenges to strengthen the entire system.