Background Prenatal alcohol exposure (PAE) has been associated with compromised interhemispheric transfer of tactile stimuli in childhood and structural changes to the corpus callosum (CC). In this study, we used a finger localization task (FLT) to investigate whether interhemispheric transfer deficits persist in adolescence; whether effects of PAE on perceptual reasoning, working memory, and executive function are mediated by deficits in interhemispheric transfer of information; and whether CC size in childhood predicts FLT performance in adolescence. Methods Participants, aged 16 to 17 years, were from the Cape Town Longitudinal Cohort, whose mothers were recruited during pregnancy and interviewed regarding their alcohol use using the timeline follow‐back method. Diagnoses of fetal alcohol syndrome (FAS) and partial FAS (PFAS) were determined by two expert dysmorphologists; nonsyndromal exposed children were designated as heavily exposed (HE); those born to abstainers or light drinkers, as controls. The FLT was administered to 74 participants (12 FAS, 16 PFAS, 14 HE and 32 controls). CC size at age 9 to 12 years was available for 35 participants (7 FAS, 13 PFAS, 5 HE and 10 control). Results Although the degree of PAE was similar in the FAS, PFAS, and HE groups, only the adolescents with FAS showed more transfer‐related errors than controls in conditions in which one finger was stimulated. FLT performance mediated the effects of FAS on perceptual reasoning and executive function. In the subsample for which neuroimaging data from childhood were available, there was an association among adolescents with PAE of smaller CC volumes with more transfer‐related errors on the one‐finger/hand hidden condition, suggesting that CC damage previously seen in childhood continues to impact function through adolescence. Conclusions This study provides evidence of compromised interhemispheric transfer of information in adolescents with FAS, while those with PFAS or heavy exposed nonsyndromal individuals are apparently spared. It is the first to show that PAE effects on important aspects of cognitive function are partially mediated by deficits in the interhemispheric transfer of information. Prenatal alcohol exposure (PAE) is associated with corpus callosum (CC) changes and compromised inter‐hemispheric transfer of tactile information in childhood. Using finger localization, we found that adolescents with fetal alcohol syndrome (FAS) continued to demonstrate more transfer‐related errors, whereas those with partial FAS caught up. Among alcohol‐exposed children, transfer‐related errors increased with decreasing CC volume. PAE effects on perceptual reasoning, working memory, and executive function were mediated by inter‐hemispheric transfer deficits, indicating that childhood CC damage continues to impact function through adolescence.