Kinesin motor proteins facilitate microtubule-based transport by converting chemical energy into mechanical forces, but this activity is autoinhibited until cargo is loaded. Regulatory mechanisms underlying this autoinhibitory conformation are not well understood. Here, we show that a NEver in mitosis Kinase NEKL-3 directly phosphorylates a flexible elbow region between two coiled-coil domains connecting the motor head and tail of an intraflagellar transport kinesin, OSM-3. The phosphor-dead (PD) mutation, but not phosphor-mimic (PM) mutation, induces constitutive motility of OSM-3 in vitro. Using knock-in animals, we discovered that both PD and PM mutations shorten the sensory cilia. The constitutively active OSM-3PD fails to enter cilia and abnormally accumulates in neurites, mimicking another hyperactive mutation, OSM-3G444E. Conversely, OSM-3PM enters cilia but moves at a reduced speed, indicating an inhibitory role of elbow phosphorylation in kinesin motility. These findings highlight the crucial role of elbow phosphorylation in regulating kinesin autoinhibition.