Molting is an essential process in the nematode Caenorhabditis elegans during which the epidermal apical extracellular matrix, termed the cuticle, is detached and replaced at each larval stage. The conserved NIMA-related kinases NEKL-2/NEK8/NEK9 and NEKL-3/NEK6/NEK7, together with their ankyrin repeat partners, MLT-2/ANKS6, MLT-3/ANKS3, and MLT-4/INVS, are essential for normal molting. In nekl and mlt mutants, the old larval cuticle fails to be completely shed, leading to entrapment and growth arrest. To better understand the molecular and cellular functions of NEKLs during molting, we isolated genetic suppressors of nekl molting-defective mutants. Using two independent approaches, we identified CDC-42, a conserved Rho-family GTPase, and its effector protein kinase, SID-3/ACK1. Notably, CDC42 and ACK1 regulate actin dynamics in mammals, and actin reorganization within the worm epidermis has been proposed to be important for the molting process. Inhibition of NEKL–MLT activities led to strong defects in the distribution of actin and failure to form molting-specific apical actin bundles. Importantly, this phenotype was reverted following cdc-42 or sid-3 inhibition. In addition, repression of CDC-42 or SID-3 also suppressed nekl-associated defects in trafficking, a process that requires actin assembly and disassembly. Expression analyses indicated that components of the NEKL–MLT network colocalize with both actin and CDC-42 in specific regions of the epidermis. Moreover, NEKL–MLT components were required for the normal subcellular localization of CDC-42 in the epidermis as well as wild-type levels of CDC-42 activation. Taken together, our findings indicate that the NEKL–MLT network regulates actin through CDC-42 and its effector SID-3. Interestingly, we also observed that downregulation of CDC-42 in a wild-type background leads to molting defects, suggesting that there is a fine balance between NEKL–MLT and CDC-42–SID-3 activities in the epidermis., Author summary Protein kinases are key molecular regulators that act by modifying the structures and activities of proteins within the cell. Members of the NEK family of protein kinases regulate cell division and the formation of specialized organelles called cilia. Accordingly, mutations in the human NEK genes have been implicated in a number of diseases including cancer and maladies that result from defective cilia. To better understand the biological functions of NEK kinases, we have undertaken studies in the model system nematode, Caenorhabditis elegans. In this study, we found that NEK kinases regulate the organization of actin, a major component of the cytoskeleton and a player in many cellular processes. In the absence of normal NEK kinase activity, actin fails to form proper filamentous structures during worm development, which leads to growth arrest. Interestingly, these defects in nekl mutants can be partially reversed by simultaneously reducing the activities of CDC42 or ACK1, two conserved proteins that are key regulators of actin dynamics. Other findings suggest that NEK kinases control actin organization through functional interactions with CDC42 and ACK1. These studies provide a new link between NEK kinases and the actin cytoskeleton and, together with other reports, suggest that these functions may be conserved in humans.