Introduction: Emergency contraception (EC) is an important method for preventing unintended pregnancies. By being knowledgeable and readily available to dispense this medication, pharmacists play a crucial role in preventing unintended pregnancies, which can have significant social, economic, and health repercussions. This study aimed to assess the knowledge and perception of EC among undergraduate pharmacy students in Malaysia, examining the socio-demographic factors associated with these dependent variables. Materials and methods: A cross-sectional study was conducted among 355 pharmacy students from 20 institutions offering a Bachelor of Pharmacy (Hons.) program. The data was collected from April to June 2022. The questionnaire was formatted as a web-based questionnaire consisting of 33 questions divided into three sections. Independent t-test and one-way ANOVA was used to compare the means in student’s knowledge and perception. Chi-square test was used to identify the association between the demographic variables and the knowledge and perception. Results: Three hundred and fifty-five students participated in the survey. Participants' mean (SD) knowledge score was 5.31(2.94) of 10 items. Factors affecting the mean knowledge of participants include academic year (P<0.001), institution type (P<0.001), race (P<0.001), religion (P<0.001), residence area (P=0.013), and prior knowledge of EC (P<0.001). The mean (SD) score of perception was 36.8 (4.9) from 50. Most of the students had an average perception of EC. Conclusion: The findings indicate that the majority of students held average perceptions but lacked sufficient knowledge about EC, highlighting the need to address these knowledge gaps for the development of an effective educational program.