The transition to university is a critical period during which considerable life changes arise. Useful national data to design tailored interventions aimed at promoting health-related quality of life (HRQoL) among Moroccan students are lacking. The present study is aimed at filling this gap by investigating the levels and associated factors of HRQoL among a national sample of Moroccan university students. HRQoL was assessed using the EQ-5D-5L instrument. Data from 2759 university students were collected in a large, cross-sectional, web-based survey. All statistical analyses were conducted using the R software. The EQ-5D-5L findings showed that the majority of students rated level 1 (no problems) and level 2 (slight problems) for the "Mobility", "Self-Care", "Usual Activities", and "Pain/Discomfort" HRQoL dimensions. However, the "Anxiety/Depression" dimension was the exception; more than half (57.1%) of the students were slightly to extremely anxious or depressed. The levels of lifestyle habits were of concern among participants of this study. With respect to sedentary behaviors and physical activity, we found that approximately 80% of participants spent ≥2 h/day on different screen-based sedentary behaviors, and 60% were physically inactive. Lifestyle habits that were found to be associated with HRQoL are sleeping time, physical activity, leisure, hygiene, household activities, homework, and social media time. The multiple regression model explained 93% of the EQ-VAS score variance. The findings could be of great importance for researchers and policymakers interested in promoting health of university students.