Introduction It is now widely acknowledged that without appropriate support, young people with neurodevelopmental conditions (NDCs) are at an increased risk of many of the social and psychiatric outcomes which are known to be key drivers of physical health inequalities. Despite this, until recently relatively little attention has been paid to their physical health trajectories. There is now emerging longitudinal evidence to suggest an association between specific NDCs in childhood or adolescence and certain physical long-term conditions (LTCs) in adulthood. However, to date this literature has never been comprehensively appraised. As a result, our understanding of all the future health risks that young people with NDCs may collectively be at risk of is limited and the factors which drive these adult health outcomes also remain obscure. Methods A search strategy has been developed in collaboration with two medical librarians and will be used to conduct systematic searches of Medline, Embase, APA PsycINFO, Cumulative Index to Nursing and Allied Health Literature, and Web Of Science. Prospective longitudinal studies exploring the association between three common NDCs in childhood or adolescence (i.e., ADHD, Autism, and Tic Disorders <18 years of age) and any physical LTC in adulthood (i.e., > 18 years of age) will be selected through title and abstract review, followed by a full-text review. Data extracted will include definition of exposure and outcome, mediators or moderators investigated, confounders adjusted for, and crude and adjusted effect estimates. Risk of bias assessment will be conducted. Results will be synthesized narratively and if the data allow, a meta-analysis will also be conducted. Ethics and dissemination Ethics approval is not applicable for this study since no original data will be collected. The results of the review will be widely disseminated locally, nationally, and internationally through peer-reviewed publication, adhering to the PRISMA statement, and conference presentations.