Background <p>Polycystic ovary syndrome (PCOS) is a multifactorial disorder characterized by hyperandrogenism, ovulatory dysfunction, and metabolic disturbances. Physical exercise is known to improve metabolic and hormonal profiles, yet the optimal type and intensity remain unclear.</p> Objective <p>To compare the effects of high-intensity interval training (HIIT) versus regular-intensity training (RIT) on the free androgen index (FAI) and other hormonal and metabolic parameters in women with PCOS.</p> Methods <p>Forty-eight women with PCOS were randomly assigned to a 12-week supervised exercise program: HIIT (<i>n</i> = 24) or RIT (<i>n</i> = 24). Serum hormone and metabolic parameters were measured at baseline and post-intervention. Age was included as a covariate in analyses due to between-group differences. Clinical trial number: Not applicable.</p> Results <p>After 12 weeks, the HIIT group showed a significantly greater reduction in FAI and HOMA-IR compared with RIT (<i>p</i> &lt; 0.05). Improvements in BMI, LH/FSH ratio, and fasting insulin were also more pronounced in the HIIT group. Bonferroni corrections and effect sizes (Cohen’s d) were calculated for all multiple comparisons.</p> Conclusion <p>HIIT appears to exert superior effects on androgenic and metabolic profiles compared with RIT, suggesting its potential as an efficient, non-pharmacological intervention for PCOS management. The clinical significance of these findings supports incorporating structured HIIT protocols into individualized PCOS treatment strategies.</p> Clinical trial number <p>Not applicable.</p>