In teleost fish, sex differences in several behavioral and physiological traits have been assumed to reflect underlying sex differences in the central expression of neurotransmitter/neuromodulator-related molecules, including vasotocin (VT)/isotocin (IT), gonadotropin-releasing hormone (GnRH), and tyrosine and tryptophan hydroxylases (TH and TPH). However, the sex-dependent expression patterns of these molecules have not been fully characterized in the teleost brain. In the present study, we therefore systematically evaluated sex differences in their expression in the medaka (Oryzias latipes) brain. The most prominent sex difference was observed in vt expression in the nucleus posterior tuberis (NPT) and the posterior part of the nucleus ventral tuberis (NVT) in the hypothalamus, where the expression was completely male-specific. Male-biased expression of gnrh1, tph1, and tph2 was also evident in the supracommissural and posterior nuclei of the ventral telencephalic area (Vs/Vp), medial nucleus of the dorsal telencephalic area (Dm), and thalamic dorsal posterior nucleus (DP), respectively. In contrast, the overall expression levels of it and gnrh3 were higher in the female brain than in the male brain. Equally importantly, no conspicuous sex differences were observed in the expression of gnrh2, th1, and th2, despite several previous reports of their sex-biased expression in the brains of other teleost species. Taken together, these data have uncovered previously unidentified sex differences in the expression of VT/IT, GnRH, and TPH in the teleost brain, which may possibly be relevant to sexual dimorphism in some behavioral and/or physiological traits, and have simultaneously highlighted potential species differences in the roles of these molecules.