This systematic review and meta-analysis aimed to estimate the prevalence of amblyopia following congenital cataract surgery in children and evaluate key prognostic factors, including age at intervention, cataract phenotype, and follow-up duration. We systematically searched PubMed, EMBASE, and the Cochrane Library for studies published between January 1, 1981, and March 1, 2023. We included clinical trials, case series, and observational studies to analyze surgical timing, visual outcomes, and complications. Among 28 studies (2,167 patients, 3,371 eyes), the pooled amblyopia prevalence was 62% (95% CI: 0.55-0.69, I = 91.7%). Early surgery (≤ 8 weeks for unilateral, ≤ 12 weeks for bilateral cases) significantly reduced amblyopia risk (P < 0.001) but increased complications, notably glaucoma (26% vs. 6%, P = 0.001). In contrast, intraocular lens (IOL) implantation timing had no significant effect on visual outcomes (P = 0.096). Unilateral partial obstruction conferred a higher amblyopia prevalence than bilateral complete obstruction (68% vs. 36%, P = 0.003), and prolong amblyopia therapy beyond 6 years of age showed limited efficacy. These findings highlight the critical role of timely surgery in optimizing visual recovery, despite its association with complications. Early IOL implantation demonstrated no significant clinical benefits, and the therapeutic window for amblyopia rehabilitation in congenital cataracts is narrower than in other forms.