This study aims to explore the optimal management strategy for pediatric vanishing testes syndrome (VTS) based on pathological characteristics. We retrospectively analyzed clinical data and pathological results of children with unilateral VTS who underwent surgical treatment at our center from July 2012 to July 2023. The children were categorized into the testicular excision group and testicular preservation group based on the surgical approach. Clinical characteristics and outcomes were compared between the two groups. Pathological examination results of excised testicular tissues were collected and analyzed, and long-term follow-up was conducted. A total of 368 children were included in this study. The age of the children at the time of surgery was 27 months (range, 6–156). Among them, 267 cases (72.6%) had VTS on the left side, and 101 cases (27.4%) on the right side. There were no statistically significant differences (P > 0.05) in age, affected side, contralateral testicular hypertrophy (CTH), testicular location, and preferred surgical incision between the testicular excision group (n = 336) and the testicular preservation group (n = 32). In the preservation group, two children experienced scrotal incision infections, showing a statistically significant difference compared to the excision group (P < 0.05). Pathological examination of excised tissues revealed fibrosis as the most common finding (79.5%), followed by vas deferens involvement (67%), epididymis involvement (40.5%), calcification (38.4%), and hemosiderin deposition (17.9%). Seminiferous tubules (SNT) was present in 24 cases (7.1%), germ cells (GC)in 15 cases (4.5%), and ectopic adrenal cortical tissue(EACT) in 1 case (0.3%). VTS belongs to a type of non-palpable testes (NPT) and requires surgical exploration. Considering the risk of scrotal incision infection after preserving atrophic testicular remnants and the unpredictable malignant potential, we recommend excision.