Background: Non-suicidal self-injury (NSSI) is a growing healthcare problem. Individuals with NSSI have an increased risk of suicidality. Because of stigma, they may self-injure in secret, which means they often seek help when events have escalated to suicidal ideation or a mental disorder. Previous studies have shown that interventions delivered via mobile phone applications have the potential to reduce self-injury. This protocol outlines a trial, which examines whether the Zero Self Harm-intervention, which is based on an app created for people with NSSI, can reduce the number of NSSI-episodes, suicide ideation, and depressive symptoms. Methods: The trial will be conducted as a 6-month 2-arm, parallel-group, multicentre, pragmatic, randomized clinical superiority trial. The intervention group will receive the app and instructions on how to use it, while the control group will be allocated to a waitlist and allowed to download the app after 6 months. Participants will be asked to complete questionnaires at 3- and 6 months after date of inclusion and the primary outcome is the number of NSSI-episodes during the last month, as measured at the 3 months follow-up with the Deliberate Self-Harm Inventory. A total of 280 participants, 140 in each arm, will be included.Discussion: This trial will assess the effectiveness of the Zero Self Harm-intervention to reduce the number of NSSI episodes. If effective, the app will have the potential to support to large group of people with NSSI. NSSI is stigmatised and often done in secret. Being both discreet and anonymous, the app might be an appealing option for support. In addition, people with current or former NSSI were involved in the development of the app. The app was developed with a focus on minimizing harm, not to end NSSI, which might also make the app appealing for a broader group of users.Trial registration: ClinicalTrials.gov, NCT04463654. Registered on 7 June 2020