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The provision and usage of online and e-learning system is becoming the main challenge for many universities during COVID-19 pandemic. E-learning system such as Blackboard has several fantastic features that would be valuable for use during this COVID-19 pandemic. However, the successful usage of e-learning system relies on understanding the adoption factors as well as the main challenges that face the current e-learning systems. There is lack of agreement about the critical challenges and factors that shape the successful usage of e-learning system during COVID-19 pandemic; hence, a clear gap has been identified in the knowledge on the critical challenges and factors of e-learning usage during this pandemic. Therefore, this study aims to explore the critical challenges that face the current e-learning systems and investigate the main factors that support the usage of e-learning system during COVID-19 pandemic. This study employed the interview method using thematic analysis through NVivo software. The interview was conducted with 30 students and 31 experts in e-learning systems at six universities from Jordan and Saudi Arabia. The findings of this study offer useful suggestions for policy-makers, designers, developers and researchers, which will enable them to get better acquainted with the key aspects of the e-learning system usage successfully during COVID-19 pandemic.