BackgroundEvidence of effective early childhood obesity prevention is scarce and mainly derived from face-to-face interventions. However, the COVID-19 pandemic drastically reduced face-to-face health programmes globally. This study assessed effectiveness of a telephone-based intervention in reducing obesity risk of young children. MethodsWe adapted a study protocol (developed before the pandemic) and conducted a pragmatic randomised controlled trial of 662 women with children aged 2 years (mean age 24·06 months [SD 0·69]) during March, 2019, and October, 2021, extending the original planned intervention of 12 months to 24 months. The adapted intervention comprised five telephone-based support sessions plus text messages over a 24-month period (at child ages 24–26 months, 28–30 months, 32–34 months, 36–38 months, and 42–44 months). The intervention group (n=331) received staged telephone plus SMS support regarding healthy eating, physical activity, and information about COVID-19. The control group (n=331) received four staged mail-outs on information not related to the obesity prevention intervention, such as toilet training, language development, and sibling relationships, as a retention strategy. The intervention effects on BMI (primary outcome) and eating habits (secondary outcome), and perceived co-benefits, were evaluated using surveys and qualitative telephone interviews at 12 months and 24 months after baseline (age 2 years). The trial is registered with the Australian Clinical Trial Registry, ACTRN12618001571268. FindingsOf 662 mothers, 537 (81%) completed the follow-up assessments at 3 years, and 491 (74%) completed the follow-up assessment at 4 years. Multiple imputation analysis showed no significant difference in mean BMI between the groups. Among low-income families (ie, annual household income <AU$80 000) at age 3 years, the intervention was significantly associated with a lower mean BMI (16·26 kg/m2 [SD 2·22]) in the intervention group than in the control group (16·84 kg/m2 [2·37]; p=0·040), a difference of –0·59 (95% CI –1·15 to –0·03; p=0·040). Children in the intervention group were more likely not to eat in front of the television than the control group, with an adjusted odds ratio (aOR) of 2·00 (95% CI 1·33 to 2·99) at 3 years and an aOR of 2·50 (1·63 to 3·83) at 4 years. Qualitative interviews with 28 mothers revealed that the intervention increased their awareness, confidence, and motivation to implement healthy feeding practices, particularly for families from culturally diverse backgrounds (ie, speaking a language other than English at home). InterpretationA telephone-based intervention was well received by the mothers who participated in the study. The intervention could reduce children's BMI from low-income families. Telephone-based support targeted at low-income families and families from culturally diverse backgrounds could reduce current inequalities in childhood obesity. FundingThe trial was funded under the NSW Health Translational Research Grant Scheme 2016 (number TRGS 200) and also by a National Health and Medical Research Council Partnership grant (number 1169823).