We previously found that female aromatase knockout (ArKO) mice showed less investigation of socially relevant odours as well as reduced sexual behaviour. We now ask whether these behavioural deficits might be due to an inadequate processing of odours in female ArKO mice. Therefore, we exposed female ArKO mice to same- and opposite-sex urinary odours and determined the expression of the immediate early gene c-Fos along the main and accessory olfactory projection pathways. We included ArKO males in the present study as we previously observed that they show female-typical detection thresholds of urinary odours, suggesting a role for perinatal oestrogens in these behavioural responses. No sex or genotype differences were observed in the olfactory bulb after urine exposure. By contrast, sex differences in c-Fos responses were observed in wild-type (WT) mice following exposure to male urine in the more central regions of the olfactory pathway; only WT females showed a significant Fos induction in the amygdala, central medial pre-optic area and ventromedial hypothalamus. However, ArKO females did not show a c-Fos response to male odours in the ventromedial hypothalamus, suggesting that the processing of male odours is affected in ArKO females and thus that oestrogens may be necessary for the development of neural responses to sexually relevant odours in female mice. By contrast, c-Fos responses to either male or oestrous female urine were very similar between ArKO and WT males, pointing to a central role of androgen vs. oestrogen signalling in the male circuits that control olfactory investigation and preferences.