Many animals display marked changes in physiology and behavior on a seasonal timescale, including non-reproductive social behaviors (e.g., aggression). Previous studies from our lab suggest that the pineal hormone melatonin acts via steroid hormones to regulate seasonal aggression in Siberian hamsters (Phodopus sungorus), a species in which both males and females display increased non-breeding aggression. The neural actions of melatonin on steroids and aggressive behavior, however, are relatively unexplored. Here, we housed male and female hamsters in long-day photoperiods (LDs, characteristic of breeding season) or short-day photoperiods (SDs, characteristic of non-breeding season) and administered timed melatonin (M) or control injections. Following 10 weeks of treatment, we quantified aggressive behavior and neural steroid sensitivity by measuring the relative mRNA expression of two steroidogenic enzymes (aromatase and 5α-reductase 3) and estrogen receptor 1 in brain regions associated with aggression or reproduction [medial preoptic area (MPOA), anterior hypothalamus (AH), arcuate nucleus (ARC), and periaqueductal gray (PAG)] via quantitative PCR. Although LD-M and SD males and females displayed increased aggression and similar changes in gene expression in the ARC, there were sex-specific effects of treatment with melatonin and SDs on gene expression in the MPOA, AH, and PAG. Furthermore, males and females exhibited different relationships between neural gene expression and aggression in response to melatonin and SDs. Collectively, these findings support a role for melatonin in regulating seasonal variation in neural steroid sensitivity and aggression and reveal how distinct neuroendocrine responses may modulate a similar behavioral phenotype in male and female hamsters.