The COVID-19 pandemic has had a profound impact on the higher education industry around the world. The battle that was fought by institutions and their faculty members to move classes and programs from a face-to-face environment to an online one has resulted in a new set of challenges for them to overcome. In the context of online education, academics working in less developed countries are confronted with quite different realities than their peers working in more developed economies. This article investigates the effect that COVID-19 had on the higher education systems of Bangladesh, India, and Pakistan, three of the most important SAARC nations at a time when these countries were struggling with limited resources, unreliable infrastructure, and a pronounced “digital divide” in higher education. The literature review and in-depth interviews conducted for the purpose of this study uncovered six primary challenges. These challenges were identified as facilitating conditions, technology readiness, learning experience, mental health, concerns regarding performance improvement and sustainability. The findings presented here highlight the necessity for more government intervention and investment in order to: firstly, improve the quality of teaching and learning; and secondly, close the digital divide. Several recommendations are stated in this paper for future research to consider.