To determine the influence of waiting time on customer's satisfaction in the central pharmacy of the Hospital Nacional Dos de Mayo (HNDM), we conducted a cross-sectional study which recorded the times of each sub process of care (billing, payment in cash and delivery of drugs) through direct observation of users. We evaluated the level of user's satisfaction using a Likert scale. We included 150 users, 59% were women, and its average age was 41.4 ± 12.6 years. The average total waiting time was 37.1 ± 14.7 minutes. The waiting time was significantly higher in the sub billing process (p <0.001) and also the time that users took long queues was higher than the actual time (30.1 ± 14.0 versus 6.3 ± 4.4; p <0.001). 17.3% of the users of the central pharmacy of HNDM showed some degree of satisfaction. The waiting time that it is less than 20 minutes was a predictor of user satisfaction (OR: 4.6 [1.1-18.3], p <0.05) regardless of other factors. In conclusion, we can say that the long waiting time principally in the sub billing process, determines a low level of user satisfaction in the central pharmacy of HNDM.