eLearning has been the medium of delivery of medical educational institutions to address the scarcity of medical professionals during the COVID-19 pandemic. In this study, the Unified Theory of Acceptance and Use of Technology (UTAUT2) was extended to determine the factors affecting the acceptance of eLearning platforms to medical education in the Philippines during the COVID-19 pandemic. A total of 360 medical students voluntary participated and answered an online questionnaire that consisted of 40 questions. Structural Equation Modeling (SEM) indicated that performance expectancy was found to have the highest effect on behavioral intention, which was followed by learning value and instructor characteristics. A high behavioral intention was found to affect the actual use of eLearning platforms. Interestingly, social influence and habit were found not to be significant to behavioral intentions. This study is the first study that has explored the acceptance of eLearning platforms among medical students in the Philippines during the COVID-19 pandemic. The findings can be a theoretical guideline of the Commission on Higher Education of the Philippines for eLearning platforms. Finally, the framework would be very valuable for enhancing the open innovation in eLearning platforms in medical fields worldwide.