In addition to its regulatory role in luteinising hormone secretion, Rfamide-related peptide 3 (RFRP3) has also been reported to modulate food intake in several mammalian species. Djungarian hamsters (Phodopus sungorus), similar to other seasonal mammals, display a remarkable inhibition of RFRP3 expression in winter short-day conditions, associated with decreased food intake and bodyweight. This species is therefore a valuable model for assessing whether RFRP3 might be involved in the seasonal control of feeding behaviour and investigating its possible brain targets. We found that, although both male and female animals exhibit the same robust reduction in Rfrp expression in short- (SD) compared to long-day (LD) conditions, acute central administration of RFRP3 displays sex-dependent effects on food intake. RFRP3 increased food intake in female hamsters in SD or in LD dioestrus, but not in LD pro-oestrus, indicating that the orexigenic effect of RFRP3 is observed in conditions of low circulating oestradiol levels. In male hamsters, food intake was not changed by acute injections of RFRP3, regardless of whether animals were in SD or LD conditions. Analysing the gene expression of various metabolic neuropeptides in the brain of RFRP3-injected Djungarian hamsters revealed that Npy expression was increased in female but not in male animals. The present study suggests that, in Djungarian hamsters, RFRP3 exhibits a sex-dependent orexigenic effect possibly by inducing increased Npy expression.