Pulsatile gonadotropin-releasing hormone (GnRH), widely used to induce spermatogenesis in congenital hypogonadotropic hypogonadism (CHH) patients, can restore the pituitary-testis axis function in males with pituitary stalk interruption syndrome (PSIS). This retrospective study aimed to compare the long-term efficacy of pulsatile GnRH therapy between PSIS and CHH.Patients of PSIS (n=25) or CHH (n=64) who received pulsatile GnRH therapy ≥ 3 months were analyzed in this retrospective study. The rate of successful spermatogenesis, the median time to achieve spermatogenesis, serum gonadotropins, total testosterone (TT), and testicular size were compared.Baseline characteristics were comparable except for the lower basal testosterone, triptorelin stimulated peak luteinizing hormone (LH) and follicle-stimulating hormone (FSH) in patients with PSIS. Within similar treatment durations, significantly higher GnRH dose (p < 0.001) but lower increase in LH [2.82 (1.4, 4.55) vs. 5.89 (3.88, 8.02) IU/L, p < 0.001], TT [0.38 (0, 1.34) vs. 2.34 (1.34, 3.66) ng/mL, p < 0.001], and testicular volume (5.3 ± 4.5 vs. 8.8 ± 4.8 mL, p < 0.05) were observed in PSIS. However, spermatogenesis rate (52.0% vs. 70.3%, p > 0.05), median time of sperm appearance (14 vs. 11 months, p > 0.05), sperm concentration and progressive motility were comparable. Basal testicular volume (HR 1.13, 95% CI 1.01-1.27) and peak LH levels (HR 1.11, 95% CI 1.0-1.23) were predictors for early sperm appearance.Pulsatile GnRH therapy can improve gonad function and induce spermatogenesis in male PSIS patients, however, its efficacy may be inferior to that in CHH.Copyright © 2022. Published by Elsevier Inc.