Hormone changes across women’s menstrual cycles may lead to changes in their perceptions of chemical signals and their hormonal responses to these cues. The aim of the present study was to determine the role of menstrual cycle phase in the response to extracts of male axillary secretions (EMAS) in women. We tested healthy reproductive age and premenopausal women (n = 29). An EMAS/control solution was applied once every two hours during either the follicular or luteal phase, at which point saliva samples for luteinizing hormone (LH) and cortisol monitoring were collected. LH and cortisol concentrations were analyzed using the enzyme immunoassay (EIA) technique. Positive and Negative Affect Schedule (PANAS) and Visual Analogue Scales (VAS) scores were used to assess the participants’ moods. For the first time, we showed that EMAS may produce opposite effects on LH secretion depending on the menstrual cycle phase of the recipient. We observed a significant increase in the number of LH peaks (p = 0.0447) and their amplitudes (p = 0.0469) when EMAS was applied during the follicular phase, while the same application in the luteal phase lowered the amplitudes of LH peaks (p = 0.0382). For the first time, we showed that EMAS application increased salivary cortisol levels in reproductive age women relative to premenopausal women (p = 0.0032). PANAS scores revealed changes in positive and negative affect after EMAS application. Our data indicate the significance of the menstrual cycle phase for EMAS’ effects on LH secretion and mood, but not on cortisol secretion in women.