The study aims to evaluate students’ perceptions towards e-Learning Management System (e-LMS) in pharmacy education. A cross-sectional survey was conducted among all undergraduates enrolled at School of Pharmaceutical Sciences, Universiti Sains Malaysia. A pre-validated questionnaire consisting of two domains (demographic characteristics and students’ perception regarding the use of e-LMS) was used for data collection. Descriptive statistics were used to describe the demographic characteristics of the study respondents. Chi Square test was used to measure association between the study variables. All analysis was performed by using Predictive Analytical Software (PASW) v. 18. A total of 315 students completed the survey questionnaire with a response rate of 57.6%. Majority of the students (61.0%) accessed e-LMS to acquire lecture notes for their studies, followed by 53.3% have used e-LMS for the preparation of the assignments. Seventy eight percent of the respondents agreed that e-LMS is very useful and felt that e-LMS is making their studies easier. However, 50% of students claimed that poor network connection at the campus is a major barrier in accessing e-LMS. Moreover, 48% of the respondents disagreed that e-LMS should be taken into account as an assessment criterion for students’ grading. Students are found to be frequently engaged in using e-LMS and believed that online based learning is enhancing their academic performances. Nevertheless, students still prefer hybrid teaching methodologies than choosing traditional system or e-learning as an alone entity.