The adoption of online learning modality among Higher Education Institutions increased exponentially amid the COVID-19 pandemic. As the universities shifted from onsite learning to online learning, course satisfaction and student engagement became the emerging concern among teachers. This study was designed to determine the significant relationship between course satisfaction and student engagement in online learning during the COVID-19 pandemic in the University of Mindanao-Bansalan College, Philippines. A total of 529 university students responded to the online survey. Results showed students' high level of course satisfaction and engagement with online learning delivery. Students have the same level of satisfaction on online learning delivery quality but have different online learning engagement levels as to year level. Also, this study revealed that online course satisfaction was significantly correlated with online student engagement. Through structural equation modeling, it was further specified that online course satisfaction is significantly related to students' skills engagement, emotion engagement, participation engagement, and performance engagement as constructs of student engagement in online learning. Higher Education Institutions (HEIs) need to improve online learning delivery quality in the new normal setting amid the COVID-19 pandemic and ensure to fill the gap between those students from advantaged and underprivileged backgrounds.