Background: Evidence-based medicine (EBM) is crucial in modern healthcare. Traditional in-person courses have been the norm for EBM education, but staffing constraints make fixed-time and location-based courses challenging. A systematically flipped EBM course may enhance medical professionals' proficiency in EBM. Methods: Participants attending flipped or traditional EBM classroom from July 2017 to July 2021, completing the EBM teaching effectiveness pre- and post-test, were included. The study analyzed results of subjects completing the EBM evaluating teaching effectiveness pre-test-post-test. Results: In the study with 74 pharmacy Interns (flipped classroom: n=35, Traditional classroom: n=39) from July 2017 to July 2021, both groups significantly improved EBM assessment performance from pre- to post-test. For EBM course participants, mean scores increased from 33.04 (SD=18.739) to 65.92 (SD=14.875), p <0.001. Flipped EBM course participants showed a significant increase from a mean score of 27.09 (SD=10.86) to 53.91 (SD=16.72), p <0.001. EBM teaching method did not significantly impact performance in EBM (p=0.147). Conclusions: The teaching methods in evidence-based medicine are diverse. Considering the clinical operations of various departments within a hospital, the flipped classroom model of evidence-based medicine is an effective instructional approach that can be chosen.