Novel coronavirus disease-2019 (COVID-19) causes worldwide disruption affecting most of the university students. A sudden shift to e-learning worsens the academic stress faced by pharmacy students. The impact this change on pharmacy students stress level is not well studied. This study aims to examine the severity of academic stress among pharmacy students and the factors associated with it. A descriptive cross-sectional study was conducted among undergraduate pharmacy students in a tertiary university. An online validated self-administered questionnaire which has two sections: demographic data and academic stress level was distributed to the students’ personal emails. All the data collected were analyzed using SPSS version 26.0. Out of 102 pharmacy students participated in this study, 63.8% of the pharmacy students experienced moderate stress level followed by 23.5% of severe stress and 12.7% of mild stress. Students in year 1, as well as smoking, were two independent significant factors causing academic stress among students (p-value < 0.05). This study highlights the high level of academic stress among pharmacy students especially first year students. Therefore, school management need to develop an effective counseling module to help students alleviate academic stress.