In response to the rapid advancement of digital transformation (DX) in healthcare, pharmacists are increasingly expected to interpret and apply electronic health record (EHR) information to support clinical decision-making and patient care. Despite this shift, the integration of educational EHRs into pharmacy curricula remains limited, and their educational effectiveness is underexplored in Japan. This study implemented a structured EHR-based educational program for fourth-year pharmacy students and evaluated its impact on their clinical reasoning, interprofessional perception, and information and communications technology (ICT) literacy. Nineteen students participated in a 240-min program, featuring a pediatric Kawasaki disease case, and utilizing an educational EHR platform. The instructional design included case analysis, group discussion, role-play, and reflection. Educational outcomes were assessed using pre- and post-intervention tests; rubric-based performance evaluations; Attention, Relevance, Confidence, and Satisfaction model questionnaires; and qualitative analysis of open-ended feedback. Statistical analysis using the Wilcoxon signed-rank test revealed significant improvements in knowledge and performance metrics (p<0.05). Students reported high motivation and satisfaction, and qualitative findings highlighted the program’s effectiveness in fostering clinical thinking and team-based care perspectives. However, feedback also suggested the need for workload balance and instructional pacing refinement. These findings indicate that an EHR-based program can serve as a valuable model for developing essential competencies in pharmacy education aligned with evolving professional roles. Future iterations may benefit from incorporating flipped classroom elements, repeated exposures, and diversified assessment strategies to enhance long-term learning outcomes.