Autosomal dominant polycystic kidney disease (ADPKD) is one of the common genetic diseases caused by mutation of PKD1 and PKD2, which encode polycystin-1 (PC1) and polycystin-2 (PC2) transmembrane proteins respectively. The PC1 and PC2 form the polycystin complex in renal primary cilia. Although ciliary protein defects and ciliary malformation have been suggested as main causative factors of PKD, the ciliary defect mechanisms related to renal cyst progression are poorly understood. Here, we focused on Ciliogenesis-associated kinase-1 (CILK1), which is localized in primary cilia and regulates ciliary transport. Mutations in the CILK1 gene are known to cause various ciliopathies. However, the pathogenesis of CILK1-deficient kidney is still unknown. In our study, Kinesin light chain-3 (KLC3) is identified as a novel regulator, which promotes ciliary trafficking and cystogenesis in CILK1 deficiency-related PKD. We found that KLC3 is involved in ciliary recruitment of intraflagellar transport (IFT)-B and epidermal growth factor receptor (EGFR), which contributed to the ciliary defect involved in cyst progression. Therefore, we suggest that dysregulation of the ciliary trafficking mechanism governed by KLC3 contributes to cyst progression in CILK1 deficiency-related PKD.