Pfaffia glomerata extract (PGE) has a variety of biological activities. However, its ameliorative effect on and exact working mechanism in male sexual dysfunction are still poorly understood. This study aims to evaluate the ameliorative effect of PGE on paroxetine (PRX)-induced sexual dysfunction in male mice and uses molecular docking technology to investigate its underlying mechanism. In this work, PRX-induced sexual dysfunction was caused and PGE was gavaged in mice for 28 days. The results show that PGE significantly improved the sexual performance of mice and reduced the damage to testicular tissues. Further studies showed that PGE restored serum sex hormones to normal levels and increased nitric oxide (NO) and cyclic guanosine monophosphate (cGMP) levels as well as nitric oxide synthase (NOS) activity in penile tissues, while also decreasing phosphodiesterase-5 (PDE-5) activity, thereby maintaining normal penile erection in mice. In addition, PGE improved the activities of enzymes (LDH, ACP, and ALP) related to energy metabolism in the testis and significantly increased sperm count and viability in mice. Furthermore, the molecular docking results show that all eight compounds in PGE could form a stable complex with PDE-5 and inhibit the activity of PDE-5. In conclusion, PGE had an ameliorative effect on PRX-induced sexual dysfunction, suggesting that PGE has a potential protective effect on male sexual health.