Background <p>Balance and change of direction (COD) are essential physical capabilities for soccer players, particularly female athletes who are at increased risk of non-contact lower limb injuries due to unique neuromuscular profiles. Stroboscopic Visual Training (SVT), a method that intermittently restricts visual input, has shown promise in enhancing visual-motor integration and balance performance. However, the combined effects of SVT and agility training on balance and COD performance in female soccer players remain unclear.</p> Methods <p>A randomized controlled trial was conducted involving 30 college-aged female soccer players randomly assigned to an experimental group (SVT + agility training, <i>n</i> = 15) and a control group (agility training only, <i>n</i> = 15). Both groups trained three times per week for 12 weeks. Outcome measures included static and dynamic balance tests (Stork Stand Balance Test, Static Single Stance Test, Y-Balance Test, Sensory Organization Test, and Adaptation Test) and COD tests (5-10-5 test and Illinois Agility Test). A two-way repeated measures ANOVA was used to evaluate the effects of the intervention.</p> Results <p>Both groups showed significant improvements over time in several balance and COD parameters (all <i>p</i> &lt; 0.05). However, significant group × time interactions favored the SVT group for key static and dynamic balance outcomes, including the Stork Stand Balance Test, Static Single Stance Test under eyes-closed dominant-leg condition, Sensory Organization Test composite score, visual (VIS) and vestibular (VEST) ratios, Y-Balance Test (dominant and non-dominant legs), and Adaptation Test toe-down condition (all <i>p</i> ≤ 0.033). For example, the SVT group showed large improvements in static balance (Stork Stand Balance Test, Cohen’s d = 4.03 vs. 1.70 in the control group) and dynamic balance (Y-Balance Test composite score, dominant leg d = 2.78 vs. 1.00; non-dominant leg d = 3.01 vs. 1.23). In contrast, COD performance (5-10-5 and Illinois Agility Test) improved similarly in both groups over time, with significant main effects of time (<i>p</i> &lt; 0.05) but no significant group × time interaction (<i>p</i> &gt; 0.05), indicating that SVT did not provide additional benefits in pre-planned COD tasks beyond agility training alone.</p> Conclusion <p>A 12-week SVT combined with agility training protocol significantly enhanced balance performance beyond agility training alone in female soccer players. These findings suggest that SVT can be a valuable addition to training programs aiming to improve postural control under challenging sensory conditions. However, its impact on traditional COD tests may be limited, indicating the need for future studies incorporating reactive agility assessments.</p> Trial registration number <p>Chinese Clinical Trial Registry (ChiCTR2500103857). Registered 06 June 2025 (Retrospectively registered).</p>