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[subscript 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[subscript words]: plurals and determiners predicted MLU[subscript words] in children with CIs, at 2 and 3 years of HA, whereas feminine markers and subject-pronouns were found to best predict MLU[subscript 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.