Background Stunting, an indicator of restricted linear growth, has become a primary measure of childhood undernutrition due to its persistent high prevalence globally, and importance for health and development. Although the etiology is recognized as complex, most analyses have focused on social and biomedical determinants, with limited attention on psychological factors affecting care and nurturing in the home. We assessed whether the psychological distress of parents is related to child linear growth and stunting, and documented the associated risk factors, and examined the relationship between parental distress and behavioral and other risk factors for stunting. Methods We used data from the Indonesia National Health Survey 2013, including 46,315 children 6–59 months of age. Multivariate linear, logistic, and multilevel multinomial logistic regression, using survey weights, were used to assess the relationship between parental distress, as assessed by the WHO Self Reporting Questionnaire (SRQ20), with height-for-age z score (HAZ), stunting, and behavioral and other risk factors for stunting. Results Maternal, paternal and parental distress (i.e. both maternal and paternal distress) were associated with reduced linear growth of the children by 0.086 (95% CI -0.17, -0.00), 0.11 (95% CI -0.24, -0.02) and 0.19 (95% CI -0.37, -0.00) HAZ-scores, respectively. Maternal and paternal distress increased the risk of mild stunting (HAZ <-1) by 33% (95% CI 1.17,1.50) and 37% (95% CI 1.18,1.60), and the risk of moderate stunting (HAZ <-2) by 25% (95% CI 1.10,1.43) and 28% (95% CI 1.08,1.51]), respectively. Parental stress increased the risk of moderate stunting by 40% (95% CI 1.06,1.85). Amongst specific groups of risk factors, the proportion of HAZ-score lost was associated with socioeconomic factors (30.3%) including, low wealth, low maternal occupational status, low maternal education, rural residence, and low paternal occupational status; physiological factors (15.5%) including low maternal height, low maternal mid-upper arm circumference, being male, low paternal height; behavioral factors (8.9%) including open garbage disposal, paternal smoking, not using iodized salt; and experiencing at least one infectious diseases episode (1.1%). Conclusions Maternal, paternal and parental stress were associated with reduced linear growth of children. These findings highlight the complex etiology of stunting and suggest nutritional and other biomedical interventions are insufficient, and that promotion of mental and behavioral health programs for parents must be pursued as part of a comprehensive strategy to enhance child growth and development, i.e. improved caretaker capacity, integrated community development, improved parenting skills, as well as reduced gender discrimination, and domestic violence.