This research examines academic challenges faced by students in Higher Education during COVID-19 pandemic. The population of the study consisted of undergraduates, postgraduates and lecturers in selected universities in Uganda. The researchers adopted qualitative approach which involved the use of questionnaire and interview. 120 students and 10 lecturers participated in the study. Questionnaires using a 5 point Likert-scale were administered to all 120 respondents while interviews were conducted with 5 undergraduates, 5 postgraduates and 10 lecturers. Data analyses indicated seven main academic challenges faced by students in higher education during COVID-19 pandemic namely: lack of e-learning facilities, financial constrain, Conducive environment, teachers attitude, learning new skills, lack of interest and stress and anxiety. Based on the findings, there is need for adjustment requiring all tiers of education to respond to a new and evolving strategy in order to have a continuous flow in education process, making education accessible, affordable, anytime and anywhere, mitigating and restraining the effects of any gaps created by any form of disruption in education system