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.