The functional cerebral asymmetry (FCA) in processing targets within rapid serial visual presentation (RSVP) streams has been reported to fluctuate across the menstrual cycle, with identification of the second of two closely spaced targets being impaired when both targets occur in the left or the right hemifield stream during the luteal phase, while during the menstrual phase identification of the second target is only impaired for target pairs presented in the right hemifield stream. This fluctuation has been proposed to result from variations in estradiol levels. The current study used EEG to investigated whether the cycle-related fluctuation in RSVP target identification FCA relates to changes in early, stimulus-driven, bottom-up or in later, top down-driven aspects of FCA. While the former would be expected to become evident in the early visual evoked potentials (VEPs) P1 or N1, the latter would be evident in later event-related potentials (ERPs) such as N2pc or P3. Women performed a dual-stream RSVP task once during the menstrual phase and once during the follicular phase. Estradiol levels were determined from saliva samples. In contrast to previous findings, FCA in RSVP target identification was not affected by cycle phase. However, the impairment in second-target identification when targets where closely spaced was generally smaller during the menstrual phase than during the follicular phase. This effect was matched by shorter peak latencies of P1 VEPs for the menstrual phase, and by a reduction in the latency of the second-target P3 ERP for closely spaced relative to widely spaced target pairs, again for the menstrual phase. Results suggest that in a dual-stream RSVP setup, target identification, early stage stimulus processing, and target consolidation are affected by cycle phase, but that the asymmetry of these effects does not differ between menstrual and follicular phase. The observed cycle-related modulations in neurophysiology and behavior could relate to the effects of estradiol on the locus ceruleus norepinephrine (LC-NE) system, which is known to play a major role in arousal, attention and stress response.