The flipped classroom has become increasingly popular in health professions education. The aim of this study was to analyze its effect on learning in a pathophysiology course. Flipped classroom was introduced to teach respiratory pathophysiology in 2018. We compared the exam results in respiratory pathophysiology in 2017 and 2018 and the exam results in blood pathophysiology from both years (taught by the same teacher, in a traditional way). Groups were compared with Student's t test. Students answered a survey after finishing the term. Two hundred and one students were examined in 2018 (and 229 in 2017). Gender distribution and the qualifications obtained in general pathology (in the previous year) were comparable in both years. Results in respiratory pathophysiology were significantly better in 2018 than in 2017 (mean: 48 vs. 42 out of 100; P = 0.004), but the results in blood pathophysiology remained similar. The improvement was significant only in students who scored below the median (mean: 40 vs. 33; P = 0.009) and was more evident in male than in female students (mean: 52 vs. 44; P = 0.01) and in those who did not have an academic delay (mean 51 vs. 44; P = 0.002). Most students considered that flipped classroom was more attractive and helped them to learn more and with less effort. Flipped classroom increased medical students' knowledge acquisitions in pathophysiology. It was more beneficial to male students and those with lower qualifications with no academic delay.