Abstract Background One of the most consistent findings reported in the paediatric cochlear implant (CI) literature is the heterogeneity of language performance observed more in grammatical morphology than in lexicon or pragmatics. As most of the corpus studies addressing these issues have been conducted in English, it is unclear whether their results can be generalized to other languages. In particular, little is known about languages known for their grammatical complexity, such as French. Aims The aim of this corpus study was to compare the productive use of function words (FWs) and some agreement features (AGRs) in children with CIs and children with typical development (TD) matched for mean length of utterance in words (MLU words ), a general index of grammatical complexity, and auditory experience, as measured by hearing age (HA) and chronological age (CA), respectively. Methods & Procedures Natural speech samples from 116 monolingual French‐speaking children, including 40 children with CIs followed longitudinally and 76 TD children, were collected. FWs and AGRs were analysed using a Part of Speech Tagger (POS‐T) from the Child Language Data Exchange System (CHILDES). Outcomes & Results The two groups differed by 3 years for HA and CA. No effect of family socio‐economic status (SES) was found in the CI group. Stepwise regression analyses showed that the two groups did not share the same predictors of MLU words : plurals and determiners predicted MLU words in children with CIs, at 2 and 3 years of HA, whereas feminine markers and subject‐pronouns were found to best predict MLU words in TD children at 2 and 3 years of CA. Structural equation models (SEMs), a combination of confirmatory factor analysis (CFA) and path analysis, yielded a different hierarchical structure of grammatical relations (GRs). Selective difficulties affecting verbal clitics and other pronominal forms were found specifically in the CI group (object‐pronouns, reflexive, relative and past participles). Dependency grammar analysis confirmed these contrasting developmental profiles in multiword utterances, such as preposition/nouns, subject/verbs, and verb/determiner/nouns. Conclusions & Implications Atypical grammatical patterns in children with CIs reflect a specific architecture of syntactic dependencies of FWs underpinning morphological complexity and syntactic connectivity. Clinical implications are discussed for assessment and intervention planning. What This Paper Adds What is already known on this subject The productive use of FWs has been identified as a particular area of weakness in children with CIs compared with TD children. In addition, heterogenous grammatical performance has often been found after 1–3 years of CI use, regardless of demographic factors such as age at implantation, duration of deafness or SES. What this paper adds to existing knowledge Assessing the early building of FWs and AGRs in children with CIs helps to understand the syntactic complexity and hierarchical structure of their language. Since most corpus studies on grammatical morphology have been conducted in English, it is not clear whether their difficulties can be generalized to other languages. The French language has a system of FWs and inflections that determine the morphophonological properties of nominal and verbal forms. Early grammar learning in children with CIs born with profound deafness were compared with the two groups of TD children matched both for duration of auditory experience (i.e., HA of CI children, CA of TD children) and for MLU words . We found a similar profile between groups at 2 years but not at 3 years for HA and CA. The two groups do not share the same predictors of MLU words : namely, plurals and determiners for CI children versus feminine markers and subject pronouns for TD children. They show a different syntactic organization of GRs. Children with CIs struggle with selective difficulties affecting verbal clitics and pronominal forms (object‐pronouns, reflexive, relative and past participles). Consistent with theories of morphophonological richness and syntactic connectivity, our results support the distributional learning hypothesis of language acquisition that infants and toddlers are sensitive to FWs and AGRs at an early age. Specific components of syntactic organization are disrupted in children with CIs. What are the potential or actual clinical implications of this work? This work has potential clinical implications because it unravels the limitations of morphophonological processing in children with CIs. Its results highlight a specific difficulty in learning FWs and AGRs in a verbal inflectional morphology context.