Higher education institutions are in a consistent pursuit of technological adoption through digital transformation techniques since the beginning of the technology revolution. The transformation from traditional to eLearning education system faces the challenges of Information and Communication Technologies (ICT) and operational risks. The operational risks in ICT mainly prevent the efficient utilization of eLearning systems. In the higher education system, faculty experience in eLearning, resistance to change, and quality of the Learning Management System (LMS) are the core sources of operational risks. This study endeavors to measure the impact of operational risks in eLearning implementation in higher education institutions. We employed a quantitative research design through a self-administered survey questionnaire and used the Partial Least Square approach of Structural Equation Modeling (PLS-SEM) to analyze the data. The findings indicated that eLearning implementation is positively influenced by faculty experience in eLearning and LMS quality. However, faculty resistance is not only negatively related to eLearning implementation, but it inversely influences the LMS quality as well. The study has important practical and theoretical implications discussed in the end.