Introduction: Female athletes remain underrepresented in caffeine-based performance research, and inconsistent menstrual cycle classification further limits generalization of the current evidence. This systematic review and meta-analysis examined the effects of caffeine on physical performance in female athletes participating in intermittent sports and explored whether these effects differ between the menstrual cycle phases, within the constraints of the available literature. Methods: A systematic search was conducted (PubMed, Scopus, Web of Science) from January 2000 to September 2025. Randomized controlled trials evaluating caffeine effects on physical performance in female athletes participating in intermittent-type sports and reporting menstrual cycle phase were included. Random-effects meta-analyses using standardized mean differences were conducted and subgroup analysis by menstrual cycle phase were pre-specified. Study quality was assessed using the Physiotherapy Evidence Database scale and Risk-of-Bias tool. Results: Nine studies (n=118) were included, and six (n=82) contributed to the meta-analysis. Caffeine was associated with improvements in agility (SMD=-0.62, 95% CI [-0.98 to -0.26], I2=0%) and vertical jump (SMD=0.37, 95% CI [0.05 to 0.69], I2=0%) but not sprint performance (SMD=0.03, 95% CI [-0.36 to 0.41], I2=15.2%) with low heterogeneity across outcomes. Within-condition sub-group analyses suggested caffeine-related improvements in agility within follicular-phase samples (SMD=-0.84, 95% CI [-1.34 to -0.33]), whereas effects in the luteal phase were less certain. However, between-group analyses showed no differences in caffeine effects between menstrual cycle phases (Q [1]=1.41, p=0.24), and these findings were based on a limited and methodologically constrained evidence base. Conclusion: Caffeine was associated with improvements in vertical jump and agility in females from intermittent sports. However, the small number of studies reporting menstrual cycle details, lack of appropriate experimental designs, and absence of rigorous menstrual cycle verification limit inference regarding phase-dependent effects. These findings highlight the need for well-designed studies to robustly test whether caffeine responses differ across menstrual cycle phases. Systematic review registration: https://www.crd.york.ac.uk/PROSPERO/view/CRD42025634451.
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