Successful implementation and use of learning management systems (LMSs) have become a critical challenge for many higher education institutes during the COVID-19 pandemic. Although LMSs with lots of features were developed for universities, the success of those systems is highly related to a detailed understanding of challenges and factors influencing the use of the systems among their users. HELMS (Higher Education Learning Management System) is a countrywide LMS used for teaching and learning during the quarantine period caused by covid-19 in Afghanistan universities. As it was the first experience of Afghan universities in using the learning management systems during the pandemic, challenges were expected to appear. No previous research has been conducted on either studying the challenges of using the HELMS or investigating the factors influencing the use of HELMS during the COVID-19 pandemic in Afghanistan. Hence, there was no unified view of the potential challenges of using HELMS and factors influencing the use of the HELMS among the researchers. This research aims to investigate the challenges that face the use of HELMS and explore the factors influencing the use of HELMS among both lecturers and students. This study employed a qualitative research method by conducting semi-structured interviews with 100 participants including university management, lecturers, and students. Thematic analysis was used as a method for the analysis of qualitative data. The findings of this research will help policymakers, researchers, and practitioners in public and private universities to grasp knowledge on the successful implementation and use of LMSs during covid-19 and afterward.