Childhood malnutrition remains endemic in South Asia, although the burden varies by country. We examined the anthropometric status and risk factors for malnutrition among children aged 0–59 months through the 2015 National Nutrition Survey in Bhutan. We assessed in 1,506 children nutritional status (by
z
‐scores of height‐for‐age [HAZ], weight‐for‐height [WHZ], and weight‐for‐age [WAZ]), estimating prevalence, adjusted for survey design, of stunting, wasting, underweight, and overweight (<−2 for HAZ, WHZ, and WAZ and >2 for WHZ). Children were also assessed for pedal oedema. We conducted multivariable linear/logistic regression analysis to identify child, maternal, and household risk factors for childhood undernutrition and overweight, excluding children with oedema (1.7%). Mean (SE) HAZ, WHZ, and WAZ were −0.82 (0.13), 0.10 (0.04), and −0.42 (0.05), respectively. Prevalence of stunting, wasting, underweight, and overweight were 21.2%, 2.6%, 7.4%, and 2.6%, respectively. In multivariable regressions, risk of stunting significantly increased by age: 5.3% at <6 months (reference), 16.8% at 6–23 months (OR = 3.06, 95% CI [0.63, 14.8]), and 25.0% at 24–59 months (OR = 5.07, [1.16, 22.2]). Risk of stunting also decreased in a dose–response manner with improved maternal education. None of the examined variables were significantly associated with wasting or overweight. Despite a WHZ distribution comparable with the World Health Organization reference (with ~2.6% vs. an expected 2.5% of children beyond 2 z in each tail), stunting persists in one fifth of preschool Bhutanese children, suggesting that other nutrient deficits or nonnutritional factors may be constraining linear growth for a substantial proportion of children.