The neurobiological basis of paroxysmal kinesigenic dyskinesia (PKD) is poorly defined due to the lack of reliable neuroimaging differences that can distinguish PKD with dystonia (PKD-D) from PKD with chorea (PKD-C). Consequently, diagnosis of PKD remains largely based on the clinical phenotype. Understanding the pathophysiology of PKD may facilitate discrimination between PKD-D and PKD-C, potentially contributing to more accurate diagnosis. We conducted resting-state functional magnetic resonance imaging on patients with PKD-D (n = 22), PKD-C (n = 10), and healthy controls (n = 32). Local synchronization was measured in all 3 groups via regional homogeneity (ReHo) and evaluated using receiver operator characteristic analysis to distinguish between PKD-C and PKD-D. Cortical-basal ganglia circuitry differed significantly between the 2 groups at a specific frequency. Furthermore, the PKD-D and PKD-C patients were observed to show different spontaneous brain activity in the right precuneus, right putamen, and right angular gyrus at the slow-5 frequency band (0.01-0.027 Hz). The frequency-specific abnormal local synchronization between the 2 types of PKD offers new insights into the pathophysiology of this disorder to some extent.