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Here, we explore the effects of prenatal alcohol exposure (PAE) in adolescence. We investigated associations between meconium ethyl glucoronide (EtG) and facial malformation. For 129 children (66/63 male/female; M = 13.3, SD = 0.32, 12–14 years), PAE was implemented by newborn meconium EtG and maternal self-reports during the third trimester. Cognitive development was operationalized by standardized scores (WISC V). The EtG cut-off values were set at ≥10 ng/g (<i>n</i> = 32, 24.8% EtG10+) and ≥112 ng/g (<i>n</i> = 20, 15.5% EtG112+). The craniofacial shape was measured using FAS Facial Photographic Analysis Software. EtG10+− and EtG112+-affected children exhibited a shorter palpebral fissure length (<i>p =</i> 0.031/<i>p</i> = 0.055). Lip circularity was smaller in EtG112+-affected children (<i>p</i> = 0.026). Maternal self-reports were not associated (<i>p</i> > 0.164). Lip circularity correlated with fluid reasoning (EtG10+ <i>p =</i> 0.031; EtG112+ <i>p</i> = 0.298) and working memory (EtG10+ <i>p</i> = 0.084; EtG112+ <i>p</i> = 0.144). The present study demonstrates visible effects of the facial phenotype in exposed adolescents. Facial malformation was associated with a child’s cognitive performance in the alcohol-exposed group. The EtG biomarker was a better predictor than maternal self-reports.