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Background The objective of this study was to clarify the state of national pharmacy practice program in the 6-year course of pharmaceutical education from the students’ point of view. We will suggest the points for improvement and issues of the current pharmacy practice programs to enhance the educational effects of the pharmacy practice program. Methods The survey conducted from September 2011 to March 2012 (hereinafter referred to as “2011”) and from September 2012 to March 2013 (hereinafter referred to as “2012”) comprised 1,607 pharmacy students, who had completed the pharmacy practice program. They were asked to fill out a self-descriptive questionnaire for the purpose of investigating the content of the pharmacy practice that the students themselves experienced, guidance provided by the supervising pharmacists, and support by the university faculty staff. Results In order to clarify the factor structure of the overall results, four factors were extracted through an exploratory analysis: “satisfactory learning”, “support system of the training site (hospital)”, “support system of university”, and “dialogue with patients”. When we compared the score for each four factors between 2011 and 2012 and we found that 2012 was evaluated as significantly higher for all factors. Furthermore, opportunities for discussion and reflection with the students led to observation that 2012 exhibited significantly better results than 2011. Conclusions The students evaluations for the quality of hospital pharmacy practice have improved in 2012 compared to evaluations in 2011. Regarding the four factors of “satisfactory learning”, “support system of the training site”, “support system of university”, and “dialogue with patients”, significant differences in the results from 2011 and 2012 were observed, indicating their marked improvement.