Self-harm in young people is a public health concern connected with severe mental health problems, such as personality pathology. Currently, there are no specific evidence-based interventions available for young people who self-harm. Therefore, we developed PRe-Intervention Monitoring of Affect and Relationships in Youth (PRIMARY), a smartphone-based intervention, co-designed by clinicians and young people with lived experience of mental ill-health. This study was a multicenter, parallel groups, randomized controlled trial (RCT) comparing the PRIMARY intervention to a waiting list control group. PRIMARY comprised 28 consecutive days of questionnaires five times each day (i.e., ESM) and four weekly report sessions. Participants were randomly allocated to a study group after screening in a 1:1 ratio by an independent researcher using computer-generated randomization sequences with stratified block randomization by age (12 to 15 years / 16 to 25 years). Staff conducted assessments with all participants at baseline (Wave 1), after 28 days (Wave 2), and in a subsample after 10 weeks of subsequent specialized treatment (Wave 3). The primary outcomes were self-harm, emotion regulation, and quality of relationships. The results of this trial will clarify whether an innovative smartphone-based intervention is effective for reducing self harm and improving emotion regulation and the quality of social relationships.