The coexistence of stunting and excess weight in the same individual is defined as a double burden of malnutrition (DBM) and is associated with noncommunicable diseases. In this study, we evaluated the impact of DBM on adipokine concentrations and metabolic profiles in children compared with weight excess alone. Children were allocated to the weight excess group (n=23) [height-for-age (HAZ)>0.0, <2.0 Z score, and body mass index-for-age (BMI/I)>1.0 Z score] or DBM (n=22) group [HAZ<-1.0 Z score (including mild stunting), and BMI/I>1.0 Z score]. Lipid, glycemic profile, resistin, plasminogen activator inhibitor-1, leptin, and adiponectin concentrations were analyzed. Glycemia was significantly higher in the DBM group compared to the weight excess group [5.05 (4.76–5.31) vs. 4.57 (4.35–4.81) mmol/l], although no differences were found in insulin and homeostasis model assessment of insulin resistance (HOMA-IR). Adipokine concentrations did not differ between the groups. However, the DBM group showed higher resistin concentrations normalized by body fat mass than those of the weight excess group [1.44 (0.98–1.93) vs. 0.76 (0.55–1.45) ng/ml]. Insulin and HOMA-IR showed negative correlation with adiponectin (r=-0.590 and -0.624, respectively, both p<0.01). DBM was associated with an increased glucose and resistin concentrations adjusted by fat mass compared to that associated with excess weight alone. Therefore, this association between mild stunting and weight excess has deleterious potential for long-term metabolic function, highlighting an additional precaution against weight gain in children, especially in those with stunting.