Background: The aim of this study was to evaluate exercise physiology students’ perceptions of two simulation-based learning modules focused on communication and interpersonal skills during history taking. Methods: A prospective, repeated-measures cohort study was conducted with 15 participants. The study evaluated two simulation-based learning modules in a 1-year Graduate Diploma of Exercise Science program. Surveys were administered at four time points: prior to each module and following each module. Students rated their confidence in communication and history taking, and perception of preparedness for practice, motivation for learning, and benefits of undertaking simulation-based learning. Quantitative data were analyzed descriptively and by using repeated measures tests. Qualitative data underwent thematic analyses. Results: Students reported a significant improvement in their confidence in communication (P = 0.043) and in two parameters related to history taking (P = 0.034 and 0.035) following the completion of the two modules. There was 96% agreement that the simulation-based learning better prepared students for practice as an exercise physiologist. Significant changes occurred in all aspects of motivation for learning (P ranging from < 0.001 to 0.036) except for usefulness, where there was a ceiling effect (medians of 7 on a 7-point scale). Qualitative analysis demonstrated benefit to participants around themes of experiential learning, realism, opportunity to develop clinical skills, and debriefing. Students also made suggestions with respect to the activity structure of the simulation-based learning modules. Conclusions: The results of this study indicated that simulation-based learning employing SPs increased the confidence and preparedness of exercise physiology students for conducting history taking, a requisite exercise physiology skill. Future studies should include behavioral measures of skill attainment and include follow-up evaluation to appraise the application of these skills into clinical practice.