Purpose Phonological complexity is known to be a good index of developmental language disorder (DLD) in normal-hearing children, who have major difficulties on some complex structures. Some deaf children with cochlear implants (CIs) present a profile that evokes DLD, with persistent linguistic difficulties despite good audiological and environmental conditions. However, teasing apart what is related to auditory deficit or to language disorder remains complex. Method We compared the performance of three groups of school-age children, 33 children with CI, 22 with DLD, and 24 with typical development, on a nonword repetition (NWR) task based on phonological complexity. Children with CI were studied regarding their linguistic profile, categorized in four subgroups ranging from excellent to very poor performance. Influence of syllable length and phonological structures on the results of all the children were explored. Results The NWR task correctly distinguished children with DLD from typically developing children, and also children with CI with the poorest linguistic performance from other children with CI. However, most complex phonological structures did not reliably identify children with CI displaying a profile similar to that of children with DLD because these structures were difficult for all of the children with CI. The simplest phonological structures were better at detecting persistent language difficulties in children with CI, as they were challenging only for the children with the poorest language outcomes. Conclusions The most complex phonological structures are not good indices of language disorder in children with CI. Phonological complexity represents a gradient of difficulty that affects normal-hearing and deaf children differently.