Introduction: New Coronavirus (COVID-19) pandemic has multiple effects. We aimed in this study to assess anxiety, depression, and stress levels among university students in Saudi Arabia and associated factors. Method: We collected 5,140 participations from universities for our cross-sectional study, responders completed the demographic questions, patient health questionnaire 9 (PHQ9) for depression, generalized anxiety disorder 7 (GAD7) for anxiety, and perceived stress scale (PSS) between 24th and 30th of April 2020. Result: 80.99% were females and mean age was 21.85 years. 40.8% had significant symptoms of anxiety, 48.8% had significant symptoms of depression, and 86.7% had moderate to high perceived stress. Being Female, younger age, living in eastern region, had a relative or acquaintances with COVID-19, and had chronic medical or mental illness are associated factors with high levels of depression, anxiety, and stress. Discussion: COVID-19 pandemic negatively affected the mental health of university students. Quick and effective interventions are mandatory.