PURPOSE: To compare outcomes of in-the-bag versus ciliary sulcus secondary intraocular lens (IOL) implantation for pediatric aphakia. DESIGN: Prospective interventional case series. METHODS: SETTING: institutional. PATIENT: Two hundred and two children (355 aphakic eyes) diagnosed as congenital cataracts and undergoing cataract extraction before 24 months of age. INTERVENTION: Pediatric aphakic eyes underwent either in-the-bag or ciliary sulcus secondary IOL implantation according to the amount of residual lens capsule and were followed for three years postoperatively. MAIN OUTCOME MEASURES: Adverse events (AEs), IOL tilt and decentration, best corrected visual acuity (BCVA) in operative eye. RESULTS: One hundred forty-four eyes (40.6%, 89 children) received in-the-bag IOL implantation (capsular group) and 211 (59.4%, 132 children) underwent ciliary sulcus IOL implantation (sulcus group). Kaplan-Meier curves showed that the time-dependent incidence of glaucoma-related adverse events (GRAEs) (P=0.005) and any AEs (P=0.002) were higher in the sulcus group. In-the-bag IOL implantation was a strong protective factor against GRAE (HR, 0.08, 95CI:0.01∼0.53; P=0.009) and any AEs (HR, 0.21 95CI: 0.08∼0.57; P=0.002). Clinically significant IOL decentration (>0.4mm) was more common in the sulcus group compared to the capsular group (vertical decentration: 29.8% vs. 15.7%, P=0.005; horizontal decentration: 30.3% vs. 9.35%, P<0.001). BCVA in the capsular group was better than that in the sulcus group (logarithm of the minimum angle of resolution [LogMAR] 0.56 vs. 0.67, P=0.014). CONCLUSIONS: Compared to ciliary sulcus secondary IOL implantation, in-the-bag IOL implantation reduced AEs, and yielded better IOL centration and BCVA for pediatric aphakia.