The pandemic of Covid-19 is forcing education sector to shift rapidly to online teaching and learning around the world. In online education, Higher Education Institutes (HEIs) faced number of issues and challenges during COVID-19. Therefore, the purpose of this research study was to identify the issues and challenges faced by education institutions during Covid-19. This study used Systematic Literature Review (SLR) approach; the systematic search process resulted in 22 relevant articles published in reputable journal during 2020-21 in different research data base. These articles discussed the issues and challenges faced by education sector during Covid-19 with the help NVivo software. During SLR, this study found 25 different issues and challenges that were further divided into 10 categories. The issues and challenges faced by educational institutions during pandemic include the poor technological access, lack of technological equipment, digital illiteracy, lack of change readiness, lack of organizations support, social issues, culture and attitude issues, digital capabilities issues, poor social development, and change management issues and challenges. The urge for conducting research in education sector is imperative and deliberated like a back-bone in the development of any nation. This research study extends the current literature on issues and challenges that were embedded by Covid-19 on the education institutions throughout the world and provide a valuable insight in terms of proper implementation of ERP systems in the education sector to avoid such issues and challenges in future. This research study also highlighted the importance of proper planning of higher education institutions for such kinds of issues and challenges.