The roles of obestatin and adropin in paediatric obesity are poorly understood. We compared obestatin and adropin concentrations in younger (n = 21) and older children (n = 14) with Prader-Willi syndrome (PWS) and age and BMI-z-matched controls (n = 31). Fasting plasma obestatin and adropin were higher in younger children with PWS than controls; adropin was also higher in older children with PWS. Growth hormone treatment had no effects on obestatin or adropin in PWS. The ratio of ghrelin to obestatin declined from early to late childhood but was higher in older PWS than older controls. Adropin correlated with fasting glucose in the PWS group only. Changes in the ratio of ghrelin to obestatin may suggest changes in the processing of preproghrelin to ghrelin and obestatin during development and differential processing of preproghrelin in PWS.