With the implementation of lockdown, social distancing measures and stay home initiatives to contain the spread of COVID-19 pandemic, there was a sudden change of pedagogy in education to continue the teaching learning process. This has challenged the education system around the globe. This study was aimed to investigate the challenges faced by the students in conducting online classes during the Corona virus (COVID-19) pandemic in a Middle Secondary School in Thimphu District, Bhutan. Adopting mixed method design, the study employed the structured questionnaire to collect quantitative data and semi-structured interview to collect qualitative data. The respondents for the study comprised of 92 students from classes nine and ten selected based on the purposive random sampling technique adopted. Quantitative data collected were analyzed based on descriptive statistics in the form of percentages using SPSS software, whereas the qualitative data were analyzed based on content analysis technique. The study found that the lack of digital facilities (smart phone, laptop and television), internet facilities and personal related factors impacted the online learning negatively during the corona virus (COVID-19) pandemic. Based on the findings of this study, it offered useful suggestions to teachers, policy makers and the Ministry of Education for the smooth and quality online teaching and learning during emergencies like COVID-19 pandemic.