Flipped classroom teaching has been used by many educators to promote active learning in higher education. This andragogy is thought to increase student engagement by making them more accountable for their learning and increase time on task in the classroom. While there are several systematic reviews that point to improved student results, it remains unclear if flipped classrooms have positive learning effects in physiology education. Flipped classroom teaching was introduced in two advanced physiology subjects (advanced neuroscience, "semester 1," and cardiorespiratory and renal physiology, "semester 2"). Changing the mode of content delivery reduced the time students needed to spend listening to lectures by one-third, without sacrificing either learning content or academic standards. Higher pass rates were observed with larger number of students earning distinction and high-distinction grades. Statistically significant improvements in final grades were observed from both subjects ("semester 1": 2017, 49.28 ± 20.16; 2018, 53.29 ± 19.77, t[subscript 268] = 2.058, P = 0.0405; "semester 2": 2017, 58.87 ± 21.19; 2018, 67.91 ± 20.40, t[subscript 111] = 2.306, P = 0.023). Finally, students' perception of their learning experience remained at or above the university benchmarks (median score of [greater than] 80% for all iterations of the subjects). While the most frequent and persistent area that students suggested could be improved was reduction of content, equal numbers of students commented that no improvement in the subjects was required. Despite the generally positive attitude to recorded didactic teaching content, classroom attendance remained very low, and students did not engage with the active learning content. This suggests that more emphasis needs to be placed on promoting class attendance by developing better active learning content.