The primary cilium is a hair-like microtubule-based structure that protrudes from the surface of nearly every cell and performs a wide range of sensory functions across species. A variety of signaling receptors localize to primary cilia and receive extracellular stimuli including Hedgehog morphogens, odorants, and light. Ciliary dysfunction is known to cause human diseases termed ciliopathies, which are characterized by a broad spectrum of symptoms, including polydactyly, cranio-facial abnormalities, brain malformation, obesity, polycystic kidney, anosmia, hearing loss, and retinal degeneration; however, treatment for ciliopathies remains a clinical challenge due to a poor understanding of the underlying mechanism. The assembly, disassembly, maintenance, and function of cilia rely on ciliary protein transport systems. Recently, we identified several post-translational modification enzymes as regulators of ciliary protein transport. In this presentation, we introduce the 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.