The teaching-learning process must constantly overcome the barriers imposed by rapid scientific and technological advances, as well as changes in the profiles of students and access to information. This study intended to analyze the perceptions of students and professors of medical courses of the teaching-learning strategies used in physiology at different Brazilian universities as well as the factors that influence or hinder the learning of this discipline. Questionnaires were analyzed from 174 students and 16 professors of physiology from medical courses of 20 higher education institutions (public and private) in a southern Brazilian state. The teaching strategies most used by physiology teachers coincided with the classroom activities that students consider to have the greatest contribution to their learning (expository classes/lectures, tests and questionnaires, problem-based learning/clinical case studies, and demonstrative/practical classes). It was also evidenced that teachers’ didactic is considered as a very influencing factor for the students during their learning process, whereas the teachers pointed out daily pedagogical practice as the most relevant factor in the development of their skills within the classroom. In addition, some factors hindering the teaching-learning process of physiology were identified by the respondents, such as large amounts of information, little time for study outside the classroom, previous knowledge, and intrinsic difficulty of the discipline. Finally, students tended to study alone and generally used teachers’ slides and their own notes as study materials. The continuous assessment of the perceptions, needs, and difficulties of students and teachers plays an essential role in improving the teaching-learning process.