BACKGROUND: Many of the adverse outcomes experienced by mothers and babies are directly related to the health of the woman prior to pregnancy. This preconception period is a unique window of opportunity when women are often more motivated to optimise health and change their lifestyle in preparation for pregnancy. Several risk factors in the preconception period can contribute to adverse perinatal outcomes. These risk factors can be divided into three broad areas: biomedical, social and environmental. Mobile phone applications as a behaviour change intervention have the potential to address these risks through supporting the provision of information, healthier lifestyles and informed decision-making. The aim of this systematic review is to assess the effectiveness of mobile phone applications in promoting behaviour change and improving long-term outcomes for mother and babies, in women of reproductive age. METHODS: This review will include trials that assess any mobile phone application (app) that assist women of reproductive age to optimise health behaviours. Randomised controlled trials, quasi-randomised controlled trials and cluster-randomised trials will be included. The search strategy will use both MeSH and keyword combinations to search databases including the WHO Global Health Library, CINHAL, The Cochrane Library, Embase and MEDLINE for relevant studies. Retrieved citations will be screened independently by two authors to assess eligibility. Studies will be selected only if the intervention was commenced prior to pregnancy. Comparisons will be made including mobile phone applications versus text messaging-based communications or paper-based, face-to-face or telephone conversations and standard care or no specific intervention. The Cochrane Handbook for Systematic Reviews of Interventions will be utilised to assess the quality of included randomised studies. Primary and secondary outcomes will be compared and analysed. Results of the review will be reported using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocols (PRISMA-P) guidelines. DISCUSSION: This systematic review is the first to assess the effects of preconception mobile phone app behaviour change and educational interventions in improving future pregnancy and maternal and child outcomes, in women of reproductive age. SYSTEMATIC REVIEW REGISTRATION: PROSPERO 2017: CRD42017065903 .