To analyze the association between stable asymptomatic white matter lesions (WMLs) and the cochlear implantation (CI) effect in congenitally deaf children, 43 CI children with stable asymptomatic WMLs determined via preoperative assessments and 86 peers with normal white matter were included. Outcome measurements included closed-set Mandarin Chinese (tone, disyllable, and sentence) recognition tests; categories of auditory performance (CAPs); and speech intelligibility rating (SIR) scales at 1, 12, and 24 months post-CI. Generalized estimating equation (GEE) models were used to analyze the association between WML and outcomes. In the WML group (control group), median CAP and SIR scores were 5 (5) and 4 (4) with mean rates of tone, disyllable, and sentence recognition of 84.8% (89.0%), 87.9% (89.7%), and 85.8% (88.0%) at 24 months post-CI, respectively. Auditory and speech performance improved significantly with implant use. Compared to their peers in the control group, for the participants with stable asymptomatic WMLs, auditory and speech abilities were not significantly different (p > 0.05). Stable asymptomatic WMLs might not be associated with poor auditory and speech intelligibility post-CI, which indicates that it is feasible to use comprehensive assessments to screen suitable candidates with WMLs who are likely to present with a good prognosis.