Purpose <p>The causal relationship between childhood obesity and polycystic ovary syndrome (PCOS) risk remains unclear, despite established links between adult obesity and PCOS. This study employed a two-sample Mendelian randomization approach to examine whether childhood obesity might have a causal effect on PCOS development.</p> Methods <p>A genome-wide association study (GWAS) identifies SNPs associated with childhood obesity based on 13848 individuals of European ancestry. Data at the summary level for PCOS were obtained from a GWAS conducted by the FinnGen consortium, which included a large sample size of 118870 individuals, consisting of 642 cases and 118228 controls. MR methods including inverse variance&#xa0;weighted&#xa0;(IVW), MR-Egger,&#xa0;weighted&#xa0;median, simple&#xa0;mode, and&#xa0;weighted&#xa0;mode analysis were performed in this study. Sensitivity analyses were conducted to evaluate the precision and robustness of the findings.</p> Results <p>The impact of genetically determined childhood obesity on PCOS is substantial, as evidenced by the IVW analysis (OR = 1.507, 95% CI 1.193–1.903; <i>P</i> = 5.77 × 10⁻⁴) and the weighted median analysis (OR = 1.578, 95% CI 1.183–2.104; <i>P</i> = 1.91 × 10⁻³). The main findings were supported by sensitivity analyses, which yielded consistent estimates using the IVW and MR-Egger methods.</p> Conclusions <p>It is suggested that an elevated prevalence of childhood obesity could be associated with an increased risk of PCOS. The prevention of PCOS should be promoted in childhood populations with high obesity.&#xa0;Additional investigation is necessary to confirm these discoveries and explore the underlying biological processes.</p>