Estrogen receptors (ERα and ERβ) are crucial for the regulation of socio-sexual behaviors and the organization of sex-specific neural networks in the developing brain. However, how the distribution patterns of ERα and ERβ change throughout life is unclear. Using genetically modified ERβ-RFPtg mice, we investigated the distribution of ERα, ERβ, and their colocalization in the ventromedial nucleus of the hypothalamus (VMH), anteroventral periventricular nucleus (AVPV), and bed nucleus of stria terminalis (BNST) from postnatal days (PD) 0 to 56. ERα expression was higher in females that showed an increase after PD14 in all brain regions, whereas ERβ-RFP expression pattern was markedly different among the regions. In the VMH, ERβ-RFP was highly expressed on PD0 and PD7 but decreased drastically to very low expression afterward in both sexes. In contrast, ERβ-RFP expression was higher in females compared to males in the AVPV but lower in the BNST throughout life especially late- and post-pubertal periods. Our results demonstrating that ERα and ERβ-RFP expression changed in a sex-, age- and region-specific manner contribute to further clarification of the mechanisms underlying estrogen-dependent organization of the brain in both sexes.