The anticipated financial and health impacts of smoking exposure on children’s status of malnutrition have been of global concern. Albeit the emerging double burden of malnutrition along with the remarkably high prevalence of smokers in Indonesia, few studies have examined the impacts of parental smoking on child nutritional status. Using a balanced panel data of the Indonesia Family Life Survey (IFLS), we analyzed the extent of parental smoking effects on the likelihood of stunting, thinness, and overweight on children. We employed a Probit Random Effect Model with Mundlak correction to remove the endogeneity issue and estimate the impact of parental smoking (smoking status and smoking intensity) on child malnutrition status. The finding showed that paternal smoking status could increase child’s stunting by 3.73 percentage points and that one extra cigarette stick consumed by a father per day (paternal smoking intensity) could raise children’s probability of thinness, stunting, and overweight by 0.16, 0.24, and 0.09 percentage points, respectively. Overall, exposure to paternal smoking increases the risk of stunting, thinness, and overweight in children. Key policies in tobacco-control should be encouraged to reduce the potential long-term effects of paternal smoking on the future human capital and economic growth in the country.