The online flipped classroom (OFC) has emerged as a new teaching method in universities worldwide, which combines asynchronous and synchronous online learning. OFC differs from the traditional flipped classroom as it does not involve face-to-face interaction between teachers and students. Instead, the class meeting is conducted online, and it is focused on active and collaborative learning (e.g., discussion rather than lecturing). To evaluate the effectiveness of the Physiology OFC, we compared it with online live teaching (OLT) offered in the same school and semester. We analyzed the exam scores of the Physiology course as well as the scores for other courses offered in the same semester and after the Physiology course. We categorized the top 27% of the exam takers as high-achieving students and the bottom 27% as low-achieving students. Our analysis found no statistically significant difference between OFC and OLT in terms of overall exam scores for all students. However, high-achieving students in OFC scored higher on the total exam score and short answer questions, but the score of case study questions (CSQs) of low-achieving students was lower. Furthermore, students in OFC scored higher in Medical Immunology and courses dominated by logical thinking such as Pharmacology and Diagnostics than students in OLT. In conclusion, our findings suggest that OFC can achieve the same teaching effectiveness as OLT, with a more positive impact on high-achieving students. The positive impact extends beyond the Physiology course to other courses where logical thinking is critical. However, the lower performance of low-achieving students in CSQs highlights the need for further research to determine the reasons for their lower performance and potential strategies to improve their learning outcomes.