Purpose <p>Fluctuations in sex hormones across the menstrual cycle may influence immune regulation in female athletes; however, evidence regarding phase-specific mucosal immune responses to routine physical training remains limited. This study compared acute changes in salivary immune and hormonal markers induced by routine team-based physical training between the follicular and luteal phases in elite female athletes.</p> Methods <p>Twenty-five athletes completed comparable routine physical training sessions during both menstrual phases. Unstimulated whole saliva was collected before and after each routine physical training session during the mid-follicular (day 10.3 ± 2.7) and mid-luteal (day 23.6 ± 3.7) phases to determine the concentrations of secretory immunoglobulin A (SIgA), lactoferrin (LF), α-amylase (sAA), nitric oxide (NO), estradiol, progesterone, testosterone, and cortisol. Data were analyzed using two-way repeated-measures ANOVA with Bonferroni adjustment.</p> Results <p>Progesterone and LF concentrations were significantly higher during the luteal phase, whereas the testosterone-to-cortisol ratio at rest was greater during the follicular phase. Following training, SIgA, LF, and cortisol concentrations decreased, while sAA increased, with no significant change observed in NO. These responses were comparable between menstrual phases.</p> Conclusion <p>Routine physical training acutely altered salivary immune and stress-related markers in elite female athletes irrespective of menstrual phase. Higher LF concentrations during the luteal phase suggest a possible phase-related difference in innate mucosal immune status. The physiological significance of the higher follicular-phase resting T/C ratio requires further investigation.</p>