Aim: The study examined the effects of emergency online education on the mental wellbeing of university students during COVID-19 pandemic. Subject and Method: The fast spread of COVID-19 forced universities to shift from conventional pedagogy to online education. Many students, however, encountered mental challenges during this transition. To examine anxiety caused by the pandemic and the lockdown policies, a questionnaire was developed and evaluated by five experts in psychology, management, and education before it was administered through WhatsApp and Facebook to a convenience sample of 1,749 students from eight universities in Jordan during the period of April 7, 2020 and May 28, 2020. Cronbach Alpha level of the questionnaire was acceptable at level α = 0.893. The study was fully approved by the Institutional Review Board and SPSS V26 was used to perform univariate and multivariate statistics. Results: Online education resulted in anxiety and other mental health concerns for over 83% of the students. Nine factors explain students' anxiety: worries about finances, owning a personal computer, logistical requirements, social impact, family income, anxiety about the future, teachers' roles, students' technical knowledge, housing arrangements, technical requirements, awareness, and technical knowledge of teachers. Conclusion: As the pandemic continues to be a serious threat, anxiety and other mental problems if not managed, can produce more health complications for students. Therefore, universities need effective remedial procedures for protecting students' mental health during and after the pandemic.