The COVID-19 global pandemic has affected all aspects of human life, with education, not an exception. In an attempt to stop the SARS-CoV-2 spreading like wildfire, the Government of Nepal has implemented nationwide lockdowns since March 24, 2020, that have enforced schools and universities to shut down. As a consequence, more than four hundred thousand students of various levels in higher education institutions (HEIs) are in a dilemma about restoring the situation. Several HEIs, nationwide, have leaped forward from the traditional concept of learning—limited within the boundary of the classroom—to choosing digital platforms as an alternative means of teaching because of the pandemic. For this research, the descriptive and inferential analysis was carried out to investigate the effects and challenges of learning via digital platforms during this pandemic. Data were collected from students and faculty at various levels of higher education and analyzed statistically with different factors using t-test and ANOVA, and variables were found to be approximately normally distributed. The study revealed that 70% of the respondents had access to the Internet, but 36% of the Internet accessed did not continue online classes due to unexpected disturbance in Internet and electrical connectivity. Likewise, 65% of students did not feel comfortable with online classes, and among attendees of online classes, 78% of students want to meet the instructor for a better understanding of course matters. According to the analytic hierarchy process (AHP) model, three factors, such as institutional policy, internet access, and poverty, are found to be significant factors affecting the online higher education systems in Nepal. On the brighter side, this outbreak has brought ample opportunities to reform the conventional teaching-learning paradigm in Nepal.