The length of the menstrual cycle (MC) varies among women, with an average regularity between 21 and 40 days. Six temporal frames can be observed within the monthly cycle, based on the fluctuations of the hormone levels. These fluctuations are accompanied by alterations in the central nervous system (CNS) and autonomic nervous system (ANS) and can be quantified using psychophysiological techniques. In this systematic review, we discussed the studies conducted with healthy females that examined aspects associated with the functions of the ANS and the CNS, including psychological, emotional, behavioral, hormonal, and perceptive variables, relating their possible changes and alterations to different phases of the MC. The PubMed and EBSCO databases were searched for articles published between January 2010 and September 2020. The Preferred Reporting Items for Systematic Reviews and MetaAnalyses (PRISMA) was applied. A total of 64 studies investigating ANS and CNS or perceptual systems across the MC were included in this review. Several studies found more alterations in the heart rate variability components during the days following ovulation compared to the days of the follicular phase. Behavioral alterations included a decrease in the percentage of REM sleep during the mid-luteal phase and an increase in calorie intake during the late-luteal phase compared to that in the follicular phase. Additionally, the reward system was found to be engaged to a greater extent during the luteal phase than during the follicular phase. The results differed considerably for many cognitive, behavioral, and autonomic variables. No significant alterations were found in most perceptual systems. A variegated picture emerged from the results of the various studies that applied different methodologies and measurements. The results suggested a new methodology that uses the temporal dimension for investigating the interactions between biological systems and psychological effects.