Identification of prognostic factors for swallowing recovery in patients with post-stroke dysphagia is crucial for determining therapeutic strategies. We aimed at exploring hyoid kinematic features of poor swallowing prognosis in patients with post-stroke dysphagia. Of 122 patients who experienced dysphagia following ischemic stroke, 18 with poor prognosis, and 18 age- and sex-matched patients with good prognosis were selected and retrospectively reviewed. Positional data of the hyoid bone during swallowing were obtained from the initial videofluoroscopic swallowing study after stroke onset. Normalized hyoid profiles of displacement/velocity and direction angle were analyzed using functional regression analysis, and maximal or mean values were compared between the good and poor prognosis patient groups. Kinematic analysis showed that maximal horizontal displacement (P = 0.031) and velocity (P = 0.034) in forward hyoid motions were significantly reduced in patients with poor prognosis compared to those with good prognosis. Mean direction angle for the initial swallowing phase was significantly lower in patients with poor prognosis than in those with good prognosis (P = 0.0498). Our study revealed that reduced horizontal forward and altered initial backward motions of the hyoid bone during swallowing can be novel kinematic features indicating poor swallowing prognosis in patients with post-stroke dysphagia.