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In this in vitro gradient perfusion study, we determined whether there is a functional relationship between oestradiol and the arginine vasotocin/isotocin (AVT/IT) system in the female round goby (Neogobius melanostomus). Brain explants were perfused in medium supplemented with 17β-oestradiol (E2) at doses mimicking the plasma levels of this hormone in nature during the spawning-capable phase and regressing phase. We aimed to establish which pathway, genomic or non-genomic, is involved in this mechanism in different reproductive phases. For this purpose, brain explants were perfused in medium supplemented with Fulvestrant (ICI 182.780) or Actinomycin D (Act D) separately or in combination with E2. The contents of AVT and IT in the perfusion media were determined using high-performance liquid chromatography (HPLC) with fluorescence and UV detection. During the spawning-capable phase, the effect of E2 on AVT release is mediated through oestrogen receptors (ERs) via both genomic and non-genomic pathways, while IT release is mediated through ERs via a genomic pathway only. In the regressing phase, release of both nonapeptides is mediated through ERs via a genomic pathway. This is the first study to present a feasible mechanism of oestradiol action on the AVT/IT system in female fish during different phases of the reproductive cycle.