Background: Sleep hygiene protocols (SHPs) have been shown to improve sleep and stress regulation; however, the role of cortisol in shaping downstream physiological and performance adaptations remains unclear. This study primarily examined the effects of a short-term SHP on sleep duration and salivary cortisol responses across resting, pre-exercise, and post-exercise states in female collegiate soccer players and, secondarily, whether cortisol statistically mediated selected aerobic and anaerobic performance outcomes. Methods: Fourteen players (22.1 ± 3.3 y; 157.8 ± 6.0 cm; 53.5 ± 3.9 kg) completed a randomised, counterbalanced crossover study comparing habitual sleep (no sleep hygiene protocol; nSHP) with a comprehensive SHP incorporating environmental, behavioural, and educational strategies. Salivary cortisol was sampled one hour post-waking and 30 min pre- and 15 min post-exercise during standardised testing sessions. Performance outcomes included vertical jump, sprint performance (40 m and repeated sprints [RAST]), and the Yo-Yo Intermittent Recovery Test Level 1. Linear mixed-effects models assessed cortisol responses, and mediation analyses explored cortisol–performance relationships. Results: After SHP, perceived (7.87 h vs. 6.5 h; p = 0.002, ESg = 1.0) and calculated sleep duration (8.5 h vs. 6.9 h; p = 0.004, ESg = 0.95) increased significantly. Cortisol was markedly lower following SHP at selected timepoints, including before RAST (−43.05%, p = 0.006, ESg = 0.84), with additional timepoint-specific, condition-dependent differences post-anaerobic and post-aerobic exercise (Δ = 7.37 and 5.98 nmol·L−1, respectively; p < 0.001). Vertical jump height demonstrated significant total (9.92 cm, p = 0.002) and direct effects (7.72 cm, p = 0.034), and peak repeated-sprint performance showed a significant direct effect (p = 0.026). Cortisol did not significantly mediate any performance outcomes (ACME p > 0.05). Conclusions: Short-term sleep hygiene is associated with increased sleep duration, timepoint-specific modulation of cortisol responses, and selected anaerobic performance benefits; however, these effects were not explained by measured cortisol responses and are unlikely to be sustained without ongoing reinforcement or support, particularly in athletic populations.