Intra-abdominal testis (IAT) remains a challenging and controversial subset within the management of cryptorchidism. While Fowler-Stephens orchidopexy (FSO) is still being advocated as the gold standard for the treatment of this entity, there is new and conflicting evidence on the comparative outcomes between single- or two-stage laparoscopic FSO (LFSO). The aim of the study is to investigate whether staging has benefits in children receiving LFSO. We searched the PubMed, Medline, Embase, and Cochrane Trials databases for studies comparing single- with two-stage LFSO in children from January 1, 1995 to December 31, 2023. We assessed the identified studies for quality and performed a systematic review and meta-analysis in accordance with the Preferred Reporting of Systematic Reviews and Meta-Analyses. The main outcome measures examined were success rate (in terms of the scrotal position of the testis) and testicular atrophy, which were analyzed using fixed effect models. We included 17 eligible studies that involved a total of 499 operated testes. The overall success rates of single- and two-stage LFSO were 79.4 and 90.3%, respectively. The overall testicular atrophy rates of single- and two-stage LFSO were 17.3 and 11%, respectively. Fixed effect model analysis showed that two-stage LFSO is significantly superior to single-stage LFSO in overall success rate (odds ratio [OR: 2.57]; 95% confidence interval [CI]: 1.50-4.39, p = 0.0006) and testicular atrophy rate (OR: 0.48; 95% CI: 0.28-0.79, p = 0.004). There is no heterogeneity in the reports, and the funnel plot showed no publication bias. Two-stage LFSO remains the first choice of operation for children with a high IAT, with a significantly higher success rate and a lower testicular atrophy rate.