Introduction: The prognosis of first episode psychosis (FEP), which is a severe disorder, can be notably impaired by patients' disengagement from healthcare providers. Coordinated specialty care with case management is now considered as the gold standard in this population, but there are still challenges for engagement with subsequent functional impairments. Youth-friendly and patient-centred clinical approaches are sought to improve engagement in patients with FEP. Mobile applications are widely used by young people, including patients with FEP, and can increase the youth friendliness of clinical tools. We hypothesise that a co-designed mobile application used during case management can improve functioning in patients with FEP as compared with usual case management practices. Methods and analysis: A mobile case management application for planning and monitoring individualised care objectives will be co-designed with patients, caregivers and health professionals in a recovery-oriented approach. The application will be compared with usual case management practices in a multicentre, two-arm and parallel groups clinical trial. Patients will be recruited by specialised FEP teams. Impact on functioning will be assessed using the Personal and Social Performance Scale; the variation between baseline and 12 months in each group (control and active) will be the primary outcome. Ethics and dissemination: This study has been approved by the Inserm Institutional Review Board IRB00003888 (Comité d'évaluation éthique de l'INSERM, reference number 20-647). The results of the study will be published in a peer-reviewed journal and presented at national and international conferences. We will also communicate the results to patients and family representatives' associations. An optimised version of the application will be then disseminated through the French FEP network (Transition Network). Trial registration number: ClinicalTrials.gov: NCT04657380.