This research investigates the educational challenges faced by high school students in Nepal during the COVID-19 pandemic across gender, caste/ethnicity, and rural-urban areas. Using the questionnaire survey of 227 students in two secondary schools, one each from the rural and urban areas, this study uncovers the learning gaps through a comprehensive examination of health impacts, overall study levels, parental education, and time allocation to household chores, and unveils complex inequalities. Findings reveal rural-urban gaps, where rural students struggle with limited access to quality education, exacerbated by disparities in parental education and increased domestic responsibilities, particularly for female students. The impact of the pandemic varies across caste and ethnic groups, emphasizing the need for tailored interventions that consider diverse sociocultural contexts. Implications for policymakers include strategic investments in infrastructure, teacher training, and digitalization to bridge the rural-urban gap. It is important to implement policies that address the gender-specific challenges faced by female students, promote parental education, and enhance disaster preparedness. As Nepal deals with the changes in education after the pandemic, this study serves as one of the key references for transformative policies and interventions, fostering resilience, inclusivity, and equitable educational opportunities for all.