Clostridioides difficile flagellin (FliC) is associated with toxin gene expression, bacterial colonization and virulence, and is also involved in pleiotropic gene regulation during in vivo infection. However, how fliC expression is regulated and how FliC modulates C. difficile pathogenicity remain unclear. In other bacterial species, FliC participates in a regulatory network with FliW and CsrA to regulate motility. Currently, studies investigating the role of fliC in C. difficile physiology were performed with motile strains. Despite its canonical role in motility, we found fliC is highly conserved in non-motile C. difficile strains that have jettisoned most flagellar assembly genes. We therefore investigated the roles of fliC in pathogenesis and physiology in the non-motile clade 5 ribotype 078 strain C. difficile 1015 (CD1015). We determined that fliC was expressed in CD1015 and the regulatory role of fliC on toxin production is independent of functional flagella and motility. We showed protein-protein interactions between FliW-FliC and FliW-CsrA using a bacterial two-hybrid system and identified the required binding site for CsrA post-transcriptional regulation in the 5′ untranslated region of the fliC transcript. Analysis of mutations in fliC, fliW and csrA (and all combinations) on C. difficile pathogenesis indicated that FliW plays a central role in C. difficile virulence as animals infected with strains carrying a deletion of fliW showed decreased survival and increased disease severity. This work highlights that key proteins involved in flagellar biosynthesis retain their regulatory roles in pathogenesis independent of their functions in motility.