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Self-efficacy in higher education (i.e., the belief in one's ability to achieve academic goals) is positively related to academic performance, motivation, and improved indicators of adaptation to the academic environment. However, challenges in higher education can affect students' mental health, emphasizing the importance of self-efficacy in preventing mental health problems. Studies suggest that knowledge in neurosciences influences students' perception of efficacy and motivation to achieve academic success. The aim of the present study is to investigate the impact of a neuroscience course on the academic development of undergraduate students, focusing on indicators of academic experiences, self-efficacy, and mental health. To achieve this objective, this study proposes the implementation of an online neuroscience course, evaluating its impact on academic experiences, self-efficacy, and mental health indicators of higher education students. For this purpose, an online and asynchronous neuroscience course was implemented, and its impact was evaluated through an experimental and longitudinal design. The study involved 124 undergraduate students (18–29 years old), divided into a control group (n = 62) and an experimental group (n = 62). As for the results, the Academic Experiences Questionnaire – reduced version (QVA-r) showed that the course positively impacted academic adaptation, strengthening study strategies and promoting personal well-being. The Self-Efficacy in Higher Education Scale (AEFS) showed significant improvement in the experimental group, both in the total score and in the academic, training regulation, proactive actions, and academic management dimensions. The Depression, Anxiety and Stress Scale (DASS-21) indicated that the intervention may have contributed to the reduction of anxiety and stress symptoms. Pedagogical effectiveness was confirmed by the significant increase in students' performance on the general neuroscience knowledge questionnaire and on the questionnaires for each module. Participants' perception reinforced these findings: the Instructional Materials Motivation Survey – Brazilian version (IMMS-BRV) recorded high levels of situational motivation, while the Instructional Procedures Reaction Scale (ERPI) and the Results Reaction Scale (ERR) showed consistently high satisfaction indices. The findings suggest that exposure to a neuroscience course can function as a tool for improving self-efficacy, promoting more positive academic experiences, and contributing to the improvement of students' mental health.