Background: Mental disorders and their symptoms are highly prevalent in the university student population, and the transition from secondary to tertiary education is associated with a rise in mental health problems. Existing web-based interventions for the prevention of common mental disorders in student populations often focus on just one disorder and have not been designed specifically for students. There is thus a need for transdiagnostic, student-specific preventative interventions that can be widely disseminated. This two-arm, parallel group randomised controlled trial aims to evaluate the effectiveness and cost-effectiveness of a web-based transdiagnostic mental health problem prevention programme (PLUS) across several universities in four countries. Method: Students (N = 5550) will be recruited through a variety of channels and asked to complete a personality assessment to determine whether they are at high risk for developing common mental disorders. Students at high risk will be randomly allocated to either PLUS or a control intervention, which provides practical support around issues commonly experienced at university. Students at low risk will be allocated to the control intervention. Both intervention groups will be assessed at baseline, 4 weeks, 3 months, 6 months and 12 months after randomisation. Depression and generalised anxiety, assessed using the Patient Health Questionnaire and the Generalised Anxiety Disorder scales, will form the primary outcomes in this study. Secondary outcome measures include alcohol and drug use, eating behaviour, self-esteem, and quality of life. The cost-effectiveness of the intervention will also be evaluated. Conclusions: This study will contribute to understanding the role of transdiagnostic indicated web-based interventions for the prevention of common mental disorders in university students. It will also be one of the first studies to investigate the cost-effectiveness of such interventions.