The COVID-19 pandemic has seriously affected all social systems, including education in Nepal. After the government decided to implement lockdowns throughout the country, all schools and universities remained closed for a long time. To overcome the loss of education from long-term lockdowns, most of the universities of Nepal sought to continue education by using digital platforms as well as they could. The purpose of the study reported here was to examine university students' perceptions of online learning during the pandemic and identify the challenges they face while learning through online mode in rural and semi-urban areas of Nepal. Using a cross-sectional online survey design, I collected data from 8 community campuses of rural and semi-urban areas of Nepal. The participants for this study were 100 master's degree students who had been learning through various online platforms since the lockdown began. Eight of those participants were interviewed to explore their perceptions of using online learning. The result showed that the majority of the students found online learning supportive during the pandemic and they preferred the continuity of online learning even after the COVID-19 pandemic. However, they faced challenges related to technology, pedagogical skills, and the socio-economic status of the students. Based on these findings, this article argues that the effectiveness of online teaching can only be further studied by considering the effects of these other social-educational factors simultaneously.