Background <p>Preventive psychiatry requires longitudinal, transdiagnostic data from before adolescence, yet such data are scarce. We propose a nationwide, digital, open cohort in Japan to track mental health trajectories from birth to late adolescence using multi-informant assessments (caregivers and adolescents) within a transdiagnostic, biopsychosocial framework. Diagnosis-open recruitment will combine community-facing dissemination with clinically linked neurodevelopmental enrichment (e.g. autism spectrum disorder and attention-deficit/hyperactivity disorder), addressing underrepresentation of neurodivergent children and adolescents alongside neurotypical peers. An optional saliva sub-cohort will support genetic and epigenetic analyses. This design will characterize risk and protective factors and their developmental timing to inform stage-specific prevention and early intervention.</p> Methods <p>From February 2026, approximately 7,000 children and caregivers (up to ~14,000 individuals) will be recruited nationwide from community and clinical settings into a longitudinal online cohort. Eligible participants are caregivers aged ≥ 18 years of children and adolescents aged 0–18 years; adolescents aged 13–18 years will also complete self-reports. Enrollment and annual follow-ups will use a secure web platform integrated with LINE, a widely used communication app in Japan. Validated questionnaires will annually assess mental health and development: caregivers report on all children, and adolescents provide self-reports. The principal repeated transdiagnostic outcome is the caregiver-reported Strengths and Difficulties Questionnaire (SDQ) Total Difficulties score across ages 2–18 years. Adolescent self-reported scores will be analyzed as complementary informant-specific secondary outcomes. Longitudinal mixed-effects models will examine developmental changes and associations with risk and protective factors, with exploratory genetic and epigenetic analyses.</p> Discussion <p>This large longitudinal cohort will generate insights into child and adolescent mental health trajectories in Japan. Following participants from infancy through adolescence will help identify early risk and resilience indicators across traditional diagnoses. Integrating multi-informant surveys with genetic and epigenetic data will clarify how biological, psychological, and social factors interact over time. Nationwide digital recruitment aims to broaden geographic reach and reduce burden; representativeness will be empirically evaluated and findings interpreted cautiously. Results will inform the timing and targets of stage-specific preventive and early interventions in community and clinical settings.</p> Trial registration <p>Japan Registry of Clinical Trials (jRCT), jRCT1050250205. Registered on 26 January 2026.</p>