University students are at elevated risk for mental health problems. The COVID-19 pandemic and subsequent public health measures taken to combat it burdened the students' life with additional dramatic psychological impacts. The aim of this study was to investigate the psychological impacts that affected the university students in Egypt during the COVID-19 pandemic. An online survey was sent to the Egyptian university students via all means of online communication during the first week of May 2020 by using a non-probability snowball sampling. A survey included a short version Depression Anxiety Stress Scale-21 (DASS-21) and socio-demographic data. Overall, 70.5, 53.6 and 47.8% of Egyptian students had depression, anxiety and stress, respectively. Being a female, having a relative or acquaintance infected with COVID-19, having a preexisting chronic disease and lacking of psychological support from families, community and universities increase the risk of depression, anxiety and stress among Egyptian students. Being a medical student is associated with depression while, spending more time to follow news of COVID-19 pandemic is associated with increased anxiety. Egyptian students experience varying levels of psychological disturbance during COVID-19 pandemic. This study suggests that mental health of the university students should be carefully, monitored during the crisis and the universities should provide psychological-oriented services, adapted to these circumstances to mitigate its emotional impact on the students.