Aims: This study focuses on factors affecting students’ engagement, and their issues and perceptions of online education in Agricultural Economics and Agribusiness Management related curricula in Sri Lankan state universities during the COVID-19 pandemic. Place and Duration of the Study: Data were collected from university undergraduates who studied Agricultural Economics and Agribusiness Management subjects in six state universities in Sri Lanka from January 2022 to February 2022. Methodology: The primary data were collected from 215 university undergraduates in relevant discipline through a pre-tested questionnaire developed by the researcher via Google form. All the respondents were volunteered to complete the questionnaire and submitted their responses online and those responses were collected anonymously. The Factor analysis was employed in the study to generate a single value for the dependent variable and the multiple linear regression was used to understand the factors affecting Student engagement in online learning. Results: The study indicates that the majority of students showed a positive attitude toward online education. The study findings show the student-teacher interaction is a positive and significant factor in online education in Agricultural Economics and Agribusiness Management disciplines but student-to-student interaction is not a significant factor for student engagement in online education. Moreover, when the students are female and students are in their final year, they are most likely to engage in online education. The study also shows that the majority of students prefer online education even though some highlighted the negative issues. However, providing continuous and stable access to the internet connection and providing other infrastructure facilities to students and teachers are some of the main challenges in promoting online education in Sri Lanka. In addition, proper attention should be paid to assure the quality of online education to develop students holistically. Conclusion: Study concludes that building and maintaining student-teacher interaction is one of the key determinants in student engagement in online education. Also student engagement can be enhanced through a student-centered learning activities which focus on their active contribution.