In female rats, pubertal onset is associated with maturation of the medial prefrontal cortex (mPFC) and mPFC-mediated behaviours. These behavioural and anatomical changes are likely a result of the effects of oestrogens at the nuclear oestrogen receptor (ER)β, which is expressed at higher levels than the ERα isoform in the adult mPFC. Researchers have previously quantified ERβ protein and Esr2 RNA in rodents during early postnatal development and adulthood, although an adolescent-specific trajectory of this receptor in the mPFC has not been documented. Given that Esr2 expression can fluctuate in the presence or absence of oestrogens, puberty and the subsequent rise in gonadal hormones could influence levels of ERβ in the adolescent brain. To further explore this, we used RNAscope® technology to quantify the amount of Esr2 mRNA in pre-pubertal adolescent, recently post-pubertal adolescent and adult female rats. We show that Esr2 expression decreases significantly in the mPFC, striatum and motor cortex between pre-pubertal adolescence and adulthood. In the mPFC, this decrease occurs rapidly at pubertal onset, with no significant decrease in Esr2 levels between the recently post-pubertal and adult cohort. By contrast, the striatum and motor cortex had no significant differences in the amount of Esr2 mRNA between pre- and post-pubertal females. Insofar as the amount of Esr2 expression is proportional to functional ERβ, these results suggest ERβ decreases in a region-specific pattern in response to pubertal onset and highlight a role for this receptor in the maturational events that occur in the female rat mPFC at puberty.