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Primary cilia are evolutionarily conserved microtubule-based organelles that protrude from the surface of almost all cell types and decode a variety of extracellular stimuli. Ciliary dysfunction causes human diseases named ciliopathies, which span a wide range of symptoms, such as developmental and sensory abnormalities. The assembly, disassembly, maintenance and function of cilia rely on protein transport systems including intraflagellar transport (IFT) and lipidated protein intraflagellar targeting (LIFT). IFT is coordinated by three multisubunit protein complexes with molecular motors along the ciliary axoneme, while LIFT is mediated by specific chaperones that directly recognize lipid chains. Recently, it has become clear that several post-translational modification enzymes play crucial roles in the regulation of IFT and LIFT. Here, we review our current understanding of the roles of these post-translational modification enzymes in the regulation of ciliary protein trafficking as well as their regulatory mechanisms, physiological significance and involvement in human diseases., Graphical Abstract Fig. 1.The serine-threonine kinases MAK and ICK in the regulation of IFT. (A) Phylogenetic distribution of protein kinases in humans. MAK and ICK are classified into the CMGC kinase family. TK, Tyrosine kinase; TKL, Tyrosine kinase-like; STE, Homologs of yeast Sterile 7, Sterile 11, Sterile 20 kinases; CK1, Casein kinase 1; AGC, Containing PKA, PKG, PKC families; CAMK, Calcium/calmodulin-dependent protein kinase; CMGC, Containing CDK, MAPK, GSK3, CLK families. Numbers of kinases classified into each family are indicated (110). (B) Proposed model of the regulation of IFT turnaround at the ciliary tip by MAK and ICK.