NIMA-related kinases (Nrks or Neks) have emerged as key regulators of ciliogenesis. In human, mutations in Nek1 and Nek8 cause cilia-related disorders. The ciliary functions of Nrks are mostly revealed by genetic studies, however, the underlying mechanisms are not well understood. Here we show that a Chlamydomonas Nrk, CNK4 that is closely related to Nek1, regulates ciliary stability and length. CNK4 is localized to the basal body region and the flagella. cnk4 null mutant exhibited long flagella with formation of flagellar bulges. The flagella gradually became curled at the bulge formation site leading to flagellar loss. Electron microscopy shows that the curled flagella involved curling and degeneration of axonemal microtubules. cnk4 mutation resulted in flagellar increases of IFT trains as well as its accumulation at the flagellar bulges. IFT speeds were not affected, however, IFT trains frequently stalled leading to reduced IFT frequencies. These data are consistent with a model that CNK regulates microtubule dynamics and IFT to control flagellar stability and length.