Background: The prevalence of overweight is increasing worldwide in children. Multi-component interventions incorporating diet, physical activity, and behavioural change have been shown to reduce body mass index (BMI). Whilst many children have their own smartphone, the clinical effects of using smartphone applications (apps) for overweight are unknown. This systematic review aims to ascertain the effects of mHealth apps in children with overweight. Methods: We will include randomised clinical trials irrespective of publication type, year, status, or language. Children between 0 and 18 years with overweight will be included. We will compare apps targeting overweight versus sham app, no app, or usual intervention. No distinction about operative system will be considered (i.e. Android, iOS, and Window Mobile will be included). The following databases will be searched: The Cochrane Library, Excerpta Medica database (Embase), PsycINFO, PubMed, IEEE Explore, Web of Science, CINAHL, and LILACS. Primary outcomes will be body weight, quality of life, and serious adverse event. Secondary outcomes will be self-efficacy, anxiety, depression, and adverse event not considered serious. Trial inclusion, data extraction, and bias risk assessment will be conducted independently by at least two authors. We will assess risk of bias through eight domains and control risks of random errors with Trial Sequential Analysis. The quality of the evidence will be assessed using Grading of Recommendations Assessment, Development and Evaluation Tool (GRADE). Discussion: We will provide evidence of the beneficial and harmful effects of smartphone apps for children with overweight and highlight any gaps in the evidence in order to shape future potential interventions. By only including randomised clinical trials, we know that we bias our review towards benefits. Systematic review registration: PROSPERO CRD42019120210.