Prenatal alcohol exposure (PAE) associated with fetal alcohol spectrum disorders (FASD) often remain underdiagnosed. They globally cause a wide range of health and social problems leading to high costs. To outline cumulative health and social care costs in children related with PAE with and without diagnosed FASD, we followed 427 children with PAE until the age of 20 years, and 1795 controls born 1992–2001 until the year 2016. All hospital care and out-of-home care episodes, including placements in foster or residential care, were analyzed, and their costs estimated. Age-dependent patterns of diagnoses and costs of those with PAE with and without diagnosed FASD were compared to controls. Children with PAE had significantly higher risks and hospital costs for both somatic and psychiatric conditions compared with controls. Mean cumulative hospital costs were 55500€ (IQR, interquartile range, 56800€) for PAE with FASD, 30100€ (IQR 25100€) for PAE without FASD and 15600€ (IQR 12000€) for controls. Between 0–10 years, FASD was associated with higher somatic costs, whereas psychiatric costs dominated in the PAE without FASD group. FASD diagnosis was associated with lower risks of traumatic injuries, substance use disorders, and teenage pregnancies, independent of early out-of-home care, which was associated with FASD. Out-of-home care was common in PAE groups, and its costs far exceeded hospital costs: mean cumulative costs were 30-fold in FASD (610000€, IQR 375800€) and 17-fold in others with PAE (344300€, IQR 621900€) compared to controls (20500€, IQR 0€). Health and particularly social care costs associated with PAE are significant. High out-of-home care costs reflect substantial need for support for families at risk. Early diagnosis of FASD may mitigate secondary complications and associated costs emerging in adolescence. Prevention policies are urgently needed at primary, secondary and tertiary level.