This research study examines academic self-perceptions and course satisfaction among university students and associated factors during virtual classes. A cross-sectional online survey of (n = 328) undergraduate and postgraduate Saudi students who took virtual classes during the second semester of the academic year 2019-2020 and the first semester of the academic year 2020-2021 during the coronavirus disease 2019 (COVID-19) pandemic. The findings demonstrated students' scores on negative academic self-perceptions (mean (M) = 9.84; standard deviation (S.D.) = 3.09) are significantly higher in comparison to positive academic self-perceptions (M = 7.71; S.D. = 2.46) and the difference was statistically significant, t(327) = 3.69, p < 0.001. The analysis demonstrated that mean differences were significant across 'year of study', 'field of study', 'CGPA' (cumulative grade points average), 'employment status', 'on-site work' and 'being a parent of young child' (p < 0.01). Correlation analysis shows a linear positive association between perceptions of workload and low technical support with negative academic self-perceptions (p < 0.001) and an inverse relationship with positive academic self-perceptions (p < 0.001). The multiple regression analysis demonstrated that the predictor variables in the model (perceptions of workload and technical support) explain 62% variance in negative academic self-perceptions and 41% variance in positive academic self-perceptions. Furthermore, the analysis demonstrated that positive academic self-perceptions bring a 32% variance in course satisfaction. These findings underscore the importance of balancing workload during online studies in higher education and provision of adequate technical support to reduce the negative academic self-perceptions which are associated with lower levels of course satisfaction. Students' academic self-perceptions and course satisfaction during virtual studies are important factors to retain students' motivation in learning and academic performance.