Abstract: Introduction: The 2014 curricular guidelines for medical courses in Brazil aim to train humanist, critic, reflexive and ethic general practitioners, able to work at different levels of health care, primarily based within the National Unified Health System scope. To achieve this goal, higher education institutions must adopt educational technologies such as active learning methodologies, which encourage students to seek and build their own knowledge. This study aims to identify and analyze the challenges faced by Public Health teachers from two medical courses in the state of Rio Grande do Sul, Brazil in the use of Active Learning Methodologies. Method: The study was conducted as a qualitative research with a comparative case study approach, and the subjects comprised teachers of the abovementioned discipline in both universities. The information was collected through a sociodemographic questionnaire, semi-structured interviews, and semi-directed observation. The findings were assessed using thematic analysis and the questionnaire data were tabulated to assess its frequency. Result: The main findings were the understanding, on the part of the teachers, of the relevance of active methodologies in the teaching pedagogical processes, the difficulty of including them due to the lack of preparation, and the understanding of the need for the active teaching methodologies to guide the pedagogical project. Conclusion: It is concluded that the universities should be encouraged to build a continuing education project for the teaching staff in which these methodologies are assumed as the main point in the teaching practice, also contributing to reflect on the established training model, as well as to rethink the organization of the political pedagogical project of medical courses.