In this study, we aimed to (1) review the long-term outcomes of cochlear implantation in children with cochlear nerve aplasia and (2) compare the development of their auditory and speech abilities to children with normal-sized cochlear nerves. This is a retrospective case-control study. Patients who underwent unilateral cochlear implant (CI) surgery in a tertiary referral center from September 2012 to December 2018 were reviewed. The study group included 55 children with cochlear nerve aplasia diagnosed using preoperative images. The control group included 35 children with normal-sized cochlear nerves. The control group did not differ from the study group in terms of age at implantation, pre-implantation auditory and speech abilities, or the electrode array type. Cochlear implantation outcomes were assessed using a test battery, including the Categories of Auditory Performance (CAP) score, the Speech Intelligibility Rating (SIR) score, behavioral audiometry, and closed- or open-set speech recognition tests. The development of auditory and speech abilities was compared between the two groups using Generalized Linear Mixed-effect Models. The mean duration of CI usage was 4.5 years (SD = 1.5, range = 2.0 to 9.5) in the study group. The CAP scores, SIR scores, and aided hearing thresholds improved significantly post-implantation in the study group, but were significantly poorer than those in the control group. Generalized Linear Mixed-effect Models showed that the development of CAP and SIR scores was significantly slower in the study group than in the control group. Overall, 27 (49%) children with cochlear nerve aplasia had some degree of open-set speech perception skills, but the monosyllabic and bisyllabic word recognition rates were significantly lower than those in the control group. For children with cochlear nerve aplasia, auditory perception and speech intelligibility continued to improve in the long-term follow-up, but this progress was significantly slower than in children with normal-sized cochlear nerves. Most children with cochlear nerve aplasia could obtain the ability of common phrase perception and understanding simple spoken language with consistent CI usage and auditory rehabilitation.