Introduction Health behaviours such as exercise and diet strongly influence well-being and disease risk, providing the opportunity for interventions tailored to diverse individual contexts. Precise behaviour interventions are critical during adolescence and young adulthood (ages 10-25), a formative period shaping lifelong well-being. We will conduct a systematic review of just-in-time adaptive interventions (JITAIs) for health behaviour and well-being in adolescents and young adults (AYAs). A JITAI is an emerging digital health design that provides precise health support by monitoring and adjusting to individual, specific and evolving contexts in real time. Despite demonstrated potential, no published reviews have explored how JITAIs can dynamically adapt to intersectional health factors of diverse AYAs. We will identify the JITAIs' distal and proximal outcomes and their tailoring mechanisms, and report their effectiveness. We will also explore studies' considerations of health equity. This will form a comprehensive assessment of JITAIs and their role in promoting health behaviours of AYAs. We will integrate evidence to guide the development and implementation of precise, effective and equitable digital health interventions for AYAs. Methods and analysis In adherence to Preferred Reporting Items for Systematic Review and Meta-Analysis guidelines, we will conduct a systematic search across multiple databases, including CENTRAL, MEDLINE and WHO Global Index Medicus. We will include peer-reviewed studies on JITAIs targeting health of AYAs in multiple languages. Two independent reviewers will conduct screening and data extraction of study and participant characteristics, JITAI designs, health outcome measures and equity considerations. We will provide a narrative synthesis of findings and, if data allows, conduct a meta-analysis. Ethics and dissemination As we will not collect primary data, we do not require ethical approval. We will disseminate the review findings through peer-reviewed journal publication, conferences and stakeholder meetings to inform participatory research. PROSPERO registration number CRD42023473117.