One of the crucial developments in the education paradigm is the rapid growth of Information and Communications Technology (ICT). As a result, most private schools are now at the height of infusing the E-learning system and are seen as one of their advances in the learning management system. Hence, this study tries to look into a way to examine and extrapolate the integration of e-learning system and its correlation to the Junior High School students' study habits and participation. Using a descriptive-correlation method, the researchers believe in finding a link between and among variables. The study's respondents consist of one hundred and twelve (112) Junior High School students in one private school in the district of Obando, Bulacan, Philippines. The findings of the study indicate that the E-learning system is functional, reliable, usable, and efficient. The level of study habits for high school students is high, and they often participate in class discussions. In addition, a strong link or a significant correlation was observed between the integration of the E-learning system and students' study habits and participation. It is recommended that schools continue to provide teachers with training and skills services to help achieve the adoption of the E-learning framework.