Overweight and obesity in children and adolescents may impact pharmacokinetics and drug exposure. The aim of the present study was to evaluate doses of antidepressants in relation to body weight in children. We used data from the BMI Epidemiology Study (BEST) Gothenburg cohort and the National Prescribed Drug Register and included children and adolescents with a prescription of fluoxetine (n = 347) or sertraline (n = 733) and a weight measurement. For fluoxetine, individuals with overweight or obesity received slightly lower doses at first prescriptions, but not in iterated prescriptions. The weight-normalized dose was lower in individuals with overweight or obesity in first and iterated prescriptions, compared with normal weight (p < 0.01). For sertraline, there were no significant dose differences between individuals with overweight or obesity, compared with normal weight. However, pronounced differences were seen in dose per kilogram body weight in both first and iterated prescriptions (p < 0.01). We conclude that the doses of fluoxetine and sertraline were essentially similar in individuals with overweight or obesity, but the weight-normalized doses were clearly lower. Given the ongoing obesity epidemic, larger studies addressing optimal dosing in individuals with elevated weight are warranted.