Background Unintended pregnancy occurs due to incorrect or inconsistent use of a contraception method. Such pregnancies can create an economic burden on the family, society and nation as a whole. Unintended pregnancy is the underlying cause of abortion which can also result in infertility and maternal death. Adequate knowledge of emergency contraceptive pills (ECPs) and positive attitudes among the community pharmacy practitioners (CPPs) is a prerequisite for timely access of ECP, thus ultimately lessening the incidence of unintended pregnancies. This study intended to explore the knowledge, attitude and practice of CPPs toward ECPs in Kathmandu valley. Methods Cross-sectional study conducted in community pharmacies located in three districts of Kathmandu valley. A convenience sampling method was employed to interview CPPs in 227 community pharmacies using a validated questionnaire. Questionnaire assessed the demographic characteristics; knowledge, attitude and dispensing practice of the CPPs. Data were subjected to descriptive and inferential analysis using SPSS 18 (SPSS Inc., Chicago, IL, USA). Results Approximately 74.9% of respondents had a good practice on dispensing ECPs, and 70% of them counselled all the users. A significant association (p-value<0.05) was obtained between the dispensing practice of respondents and their knowledge level. ECP related knowledge was higher among the age group 40-49 years, BPharm degree holders with experience above ten years and community pharmacies located inside the city and in the Kathmandu district. After adjusting the possible confounder variables, age, degree and district of pharmacy were significantly associated with knowledge. Similarly, respondents' practice towards ECP was higher among the age group 40-49 years with experience above ten years and community pharmacies located inside the city and in the Kathmandu district. Adjusted for other variables, only community pharmacies located at Kathmandu district was significantly associated with the practice. Conclusion CPPs lacked specific important information on ECP and opined against its' availability as an OTC drug, despite good overall knowledge and positive attitude. Many thought that ECP without prescription would increase promiscuity towards sexual behaviour and result in unsafe sex along with its' repeated use. Hence, training and proper counselling strategies should be afoot to refine the delivery of service by CPPs.