The COVID-19 pandemic has caused significant disruptions in the higher education system, particularly in the learning and well-being of postgraduate students. The shift to online learning has presented unique challenges, including reduced social interaction, motivation difficulties, and technical obstacles. This study aims to investigate the impacts of the pandemic on the health and well-being of postgraduate students during online learning in Egypt. A structural equation modelling (SEM) methodology is employed to examine the relationships between online learning, physical well-being, mental well-being, sleep patterns, dietary habits, and academic performance. The findings highlight the widespread effects of the pandemic on the physical and mental health of postgraduate students, including outbreaks on campuses, heightened levels of stress and anxiety, and negative impacts on academic outcomes. The study emphasizes the importance of addressing these challenges and developing strategies to support student health and well-being in higher education during times of crisis. However, it is important to note that the study's findings are specific to postgraduate students in Egypt and may not be generalized to other student populations or geographical locations.