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Abstract Background 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. PRIMARY combines the Experience Sampling Method (ESM) with weekly report sessions. The study aims to examine the effectiveness of PRIMARY with regard to reducing self-harm, and improving emotion regulation and quality of relationships. Methods This study is a multicenter, parallel groups, randomized controlled trial (RCT) comparing the PRIMARY intervention to a waiting list control group. PRIMARY comprises 28 consecutive days of questionnaires five times each day (i.e., ESM) and four weekly report sessions. Participants will comprise 180 young people referred for treatment to the participating Dutch mental healthcare institutions and (1) are aged 12 to 25 years, and (2) engaged in ≥ 1 act of self-harm in the past year. Participants are 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 will conduct 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 are self-harm, emotion regulation, and quality of relationships. Secondary outcomes include patient and clinician satisfaction. Exploratory analyses of ESM data will examine the relationship between emotions, social relationships, and self-harm. Discussion 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. It has the potential to fill a treatment gap of interventions specifically targeting self-harm. If proven effective, it would provide an accessible, easy-to-implement, low-cost intervention for young people. Furthermore, the ESM-data will allow detailed analyses into the processes underlying self-harm, which will contribute to theoretical knowledge regarding the behavior. Trial registration ISRCTN42088538 ( https://doi.org/10.1186/ISRCTN42088538 ), retrospectively registered on the 26th of October 2022.