The global surge in childhood obesity is also evident in Indonesia. Parental body mass index (BMI) values were found to be one of the major determinants of the increasing prevalence of childhood obesity. It is uncertain if parental BMI during their offspring’s childhood significantly affects their children’s BMI trajectories into adulthood. We aimed to investigate the influence of parental BMI Z-scores on BMI trajectories of Indonesian school-aged children, with a focus on sex-specific effects. This study utilized data from the Indonesian Family Life Survey and tracked the same respondents over four time points, from wave 2 (1997–1998) to wave 5 (2014–2015). The sample of this study consisted of children aged 5–12 years in wave 2 for whom height and weight data were available. We utilized a two-level growth curve model to account for the hierarchical structure of the data, with time nested within individual children. Fathers’ BMI Z-scores in wave 2 had a pronounced influence (β = 0.31) on female children’s BMI Z-scores compared to the influence of mothers’ BMI Z-scores (β = 0.17). Mothers’ BMI Z-scores in wave 2 showed a stronger positive association with male children’s BMI Z-scores (β = 0.22) than did the father’s BMI Z-scores (β = 0.19). A significant interaction of fathers’ BMI Z-scores and years of follow-up was found for male children. As male children’s BMI Z-scores increased by year, this effect was stronger in those whose fathers’ BMI Z-scores were at a higher level. In conclusion, we found that parental BMI values profoundly influenced their children’s BMI trajectories.