Introduction Migrant women in transit face high risk of developing mental health problems such as depression and anxiety, driven by gendered social-structural factors including violence, social isolation, migration uncertainty, limited access to services and gender inequities. Although migrant women who endure such conditions have high need for mental health prevention, few evidence-based interventions are tailored to this population. Moreover, while women and children’s mental health are interconnected, few mental health interventions address parenting needs. The aim of this study is to pilot-test a novel parenting and mental health prevention intervention for migrant mothers with young children (MMC) in Tijuana, Mexico, including (a) assessing acceptability; (b) estimating effect sizes on symptoms of depression, anxiety, and parenting stress; (c) identifying which theory-based mechanisms of action predict changes in outcomes; and (d) identifying factors associated with differential intervention response.Methods and analysis ‘Mamá Empoderada’ (Mom Power) is a theory-based, trauma-informed group intervention to promote mental health and responsive parenting among mothers with young children (0–5 years). This is an evidence-based intervention that has been previously evaluated in the USA and has been recently adapted for Spanish-speaking mothers. We have recently adapted this intervention for MMC in Mexico and will conduct a pilot randomised controlled trial (RCT) of the intervention with MMC (n=100; Ntreatment=50; Ncontrol=50). The intervention group (IG) will receive 10 group and three individual sessions addressing attachment-based parenting skills, linkage to resources (eg, food, shelter), social support, and self-care and resilience over a 5-week period. The control group will receive standard of care programming and will be offered participation in the intervention following completion. Both groups will complete baseline and exit surveys, as well as follow-up surveys at 2, 4 and 6 months postintervention. Statistical analyses will compare primary (ie, symptoms of depression and anxiety; parenting stress) and intermediate outcomes (eg, resilience, service utilisation) by exposure to intervention condition.Ethics and dissemination This study is approved by the San Diego State University and El Colegio de la Frontera Norte Institutional Research Boards. Findings will inform a larger trial to evaluate intervention efficacy. In collaboration with our community partners, results will be disseminated via peer-reviewed publications; presentations; and plain-language reports, infographics, and presentations to community, clinical, and policy audiences. If efficacious, this intervention is highly promising as a novel, low-cost, and feasible model that could be implemented in border settings in Mexico, the USA and elsewhere. Amid rising population displacement and prolonged and traumatic migration journeys, this study addresses an urgent need for scalable and tailored mental health prevention for MMC in border contexts.Trial registration number NCT06468046.