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Background: Training for the fundus examination using traditional teaching is challenging, resulting in low generalist physicians' confidence in performing the funduscopic examination. There is growing evidence suggesting a flexible e-learning video approach's value in teaching physical examination procedures. However, whether the flexible e-learning video approach is superior to the traditional, face-to-face (F2F) lecture-based teaching for the funduscopic exam and the cognitive processes supporting its effectiveness has not yet been determined., Methods: We conducted a sequential explanatory mixed-method study to compare the flexible e-learning video approach's effectiveness versus the F2F lecture-based approach for teaching the funduscopic exam to medical students at Chiba University in Japan. Medical students were randomly assigned to either a flexible e-learning video approach group or a F2F lecture approach group. We then quantitatively measured the diagnostic accuracy of funduscopic findings before and after attending the specific classrooms. Next, we conducted student focus groups to explore the students' thinking processes in the flexible e-learning video approach vs. the F2F lecture-based teaching of fundus examination. The qualitative data were analyzed using the qualitative content analysis method., Results: The mean diagnostic accuracy scores in the post-test significantly increased from pre-test in the intervention group (36.6 to 63.4%, p < 0.001). Post-post comparisons across the two groups revealed a significant difference (intervention group 63.4% vs. control group 34.6%, p < 0.001). Six semi-structured focused group interviews were conducted (n = 36). In the flexible e-learning video approach group, we identified ten categories corresponding to four levels of the revised Bloom's taxonomy: remember, understand, apply, analyze. Five categories were identified in the traditional F2F lecture approach group corresponding to three revised Bloom's taxonomy levels: understand, apply, analyze. Interrater reliability was substantial (Cohen's kappa = 0.81)., Conclusions: Teaching medical students funduscopic examination using the flexible e-learning video approach leads to improved diagnostic accuracy of funduscopic examinations. The flexible e-learning video teaching method enabled higher cognitive activity levels than the traditional, lecture-based classroom, as assessed using the revised Bloom's taxonomy., Trial Registration: This study was registered with the University Hospital Medical Information Network Clinical Trials Registry on 08/02/2020 (Unique trial number: UMIN 000039434 )., (© 2021. The Author(s).)