Introduction Regular exercise has the potential to enhance university students’ mental and cognitive health. The PEAK Mood, Mind and Marks program (i.e., PEAK) is a neuroscience-informed intervention developed using the Behaviour Change Wheel to support students to exercise three or more times per week to benefit their mental and cognitive health. This pilot study assessed the impact of PEAK on exercise, mental and cognitive health, and implementation outcomes. Methods PEAK was delivered to 115 undergraduate university students throughout a 12-week university semester. The primary outcome was weekly exercise frequency. Secondary outcomes were: time spent engaged in moderate-vigorous exercise, sedentary behaviour and perceived mental health and cognitive health. All were measured via online self-report questionnaires. Qualitative interviews with 15 students investigated influences on engagement, the acceptability and appropriateness of PEAK, and its mechanisms of behaviour change. Paired t-tests, Wilcoxon Signed-Rank tests and template analysis were used to analyse quantitative and qualitative data, respectively. Results On average, 48.4% of students engaged in the recommended frequency of three or more exercise sessions per week. This proportion decreased towards the end of PEAK. Sedentary behaviour significantly decreased from baseline to end-point, and moderate-vigorous exercise significantly increased among students’ who were non-exercisers. Mental wellbeing, stress, loneliness, and sense of belonging to the university significantly improved. There were no significant changes in psychological distress. Concentration, memory, and productivity significantly improved. Sixty-eight percent of students remained engaged in one or more components of PEAK at end-point. Qualitative data indicated students found PEAK to be acceptable and appropriate, and that it improved aspects of their capability, opportunity, and motivation to exercise. Conclusions Students are receptive to an exercise-based program to support their mental and cognitive health. Students exercise frequency decreased; however, these figures are likely a conservative estimate of students exercise engagement. Students valued the neuroscience-informed approach to motivational and educational content and that the program’s goals aligned with their academic goals. Students identified numerous areas PEAK’s content and implementation can be optimised, including use of a single digital delivery platform, more opportunities to connect with peers and to expand the content’s cultural inclusivity.