We aimed to compare the diagnostic yield between temporal bone computed tomography (TBCT) and internal auditory canal MRI (IAC MRI) for the etiologic diagnosis of children with congenital single-sided deafness (SSD) and the evaluation of cochlear implant (CI) candidacy. In the original cohort, 24 subjects with congenital SSD were enrolled and underwent both TBCT and IAC MRI. We recruited an additional 22 consecutive infants with congenital SSD (the supplementary cohort) and evaluated in particular the cochlear nerve (CN) integrity using IAC MRI. Cochlear nerve deficiency (CND) was classified as ‘absent’, ‘small’, and ‘indeterminate’ via mutual comparison between optical and parameters based on the MRI results. The most common etiologies were CND in the original cohort (19 out of 24). Notably, accurate evaluations of CN status (‘small CN’ = 2, ‘indeterminate CN’ = 2), inner ear malformations, and brain abnormalities were possible only with MRI. The ‘indeterminate CN’ tended to be more frequently detected in SSD ears than in unaffected ears. MRI appeared to be more accurate than TBCT in a meticulous differentiation of CN, which is crucial for the selection of appropriate CI candidacy among congenital SSD children. Additionally, we introduced the novel concept of ‘indeterminate CN’, of which the causal relationship with SSD awaits confirmation.