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Background: Clinical Pharmacy Practice Experience (CPPE) is an important curriculum that offers students patient-centered disease prevention and treatment with evidence-based optimal pharmacotherapy for better clinical outcomes. However, few studies have evaluated the perception of pharmacy students regarding CPPE in tertiary and secondary hospitals. This study aimed to evaluate the perception of pharmacy students regarding the learning program of CPPE. Methods: The survey questionnaire consisted of 15 self-administered questions regarding pharmacy practices, barriers, and improvement of practical training. Fourteen institutional pharmacies located in seven regions responded to a survey questionnaire from March 1 to June 30, 2017. The participants were pharmacy students doing clerkship in a hospital setting. Results: The response rate was 73.6%. Thirty-five participants (22.4%) had used a hospital library, but 121 (77.6%) had never used the library for drug information resources. Eightyone (50.0%) responded that clinical knowledge and drug information was the most beneficial practice. Thirty-seven (31.1%) respondents in the tertiary hospitals and 19 (46.3%) in the secondary hospitals answered that they were filling prescriptions during the daily break. On the other hand, 72 respondents (60.5%) in the tertiary hospitals and 17 (41.5%) in the secondary hospitals did literature research to prepare for presentation. Conclusion: More students in secondary hospitals continue to fill prescriptions during the daily break, as compared to those in tertiary hospitals. Therefore, the authors suggest self-directed learning to improve clinical performance and each institution considers offering onsite or online library service to improve evidence-based CPPE for pharmacy school students.