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Research suggests that major disruptions to one's life can have negative effects on their mental wellbeing. The novel coronavirus disease (COVID-19) pandemic has caused psychological distress in various contexts of human life. Cancellation of sporting events and transition of courses to primarily online platforms can have significant impact on the lives of university student athletes during the COVID-19 pandemic, hence increasing their risk of poor mental wellbeing and loneliness. The present study aimed at determining the mental wellbeing of student-athletes in a certain university in Ghana during the COVID-19 pandemic. This descriptive cross-sectional study recruited a total of 200 participants (102 student-athletes and 98 non-athlete students). Mental wellbeing of participants in terms of depression, anxiety and stress was assessed using the Depression, Anxiety and Stress Scale (DASS-21). Statistical analysis of data revealed significant difference between the mean scores of athletes and non-athletes for all mental health variables under consideration; depression, anxiety and stress (p<0.05), with the athlete group reporting poorer mental wellbeing than the non-athlete group. The results indicated that the pandemic affected student athletes significantly more than the non-athletes. The student-athletes were comparably more depressed, anxious and stressed during the pandemic than their non-athlete counterparts. Findings from the study have implications for the development of policy guidelines by university authorities and other stakeholders to alleviate the potential threat of the pandemic to the mental wellbeing of the student population.