Early childhood overweight and obesity increased substantially in high-income countries throughout the 1980s and 1990s. The flattening or reversal of this trend since the early 2000s might conceal widening inequalities. This study aimed to identify trends in body-mass index Z score (BMIz) among children aged 1-3·5 years in Victoria (Australia), by socioeconomic status and geographical location. This repeated, cross-sectional study used deidentified records of height, weight, and demographic information from electronic databases in the Victorian Maternal and Child Health system. Data from the consultations for children aged 1, 2, and 3·5 years were included in this analysis. We removed duplicate records; records with missing data for sex, age, weight, height, or postcode; and records with postcodes that were outside of Victoria. The coprimary outcomes were trends in mean BMIz (continuous linear models) and prevalence of high BMIz (>+1; generalised linear models), estimated for six independent age-sex groups. Secondary analysis was done for the prevalence of BMIz greater than 2. Effect modification by socioeconomic status and remoteness was evaluated. Electronic data were available for 48 local government areas collected between Jan 1, 2003, and Dec 31, 2017, representing approximately 63% of the Victorian population. Overall, 1 329 520 measurements from 675 991 children were included in the analysis. There were small, significantly decreasing trends in mean BMIz across all six age-sex groups, overall and in major cities. Similar patterns were observed for some subgroups in prevalence of high BMIz. These decreasing trends appear to be partly explained by migration. Conversely, in regional areas the trends in BMIz were consistently increasing in all age-sex groups and across socioeconomic strata, although not all groups were statistically significant. Inequalities in BMIz according to socioeconomic status persisted throughout the study period, such that the children from more advantaged areas had lower mean BMIz. This study showed that at a state level, mean BMIz and prevalence of high BMIz decreased in children aged 1, 2, and 3·5 years in Victoria between 2003 and 2017. We found metropolitan-regional differences to be key source of inequality in early childhood BMIz trends, alongside area-level socioeconomic status. These findings highlight the risk that analysis of overall trends in childhood BMIz might obscure important inequalities according to, for example, remoteness, socioeconomic status, and ethnicity. Future research requires monitoring data with large population samples to adequately examine differences in prevalence and trends between population subgroups. None.