Dysphagia affects up to half of stroke patients and increases the risk of pneumonia and fatal outcomes. In order to assess swallowing difficulty, videofluoroscopic swallowing study (VFSS) has traditionally been the gold standard. The purpose of this study was to compare the patterns of post-stroke swallowing difficulties according to the vascular territories involved in the stroke. One hundred and three patients who were diagnosed with first ischemic stroke by brain magnetic resonance imaging and had swallowing difficulty were included in this study. Location of the stroke was classified into three groups: territorial anterior infarcts (TAI) (n = 62), territorial posterior infarcts (TPI) (n = 19) and white matter disease (WMD) (n = 22). Oral cavity residue existed significantly in the TAI group more than in any other groups (P = 0.017). The WMD group showed more residue in the valleculae (P = 0.002) and the TPI group showed more residue in the pyriform sinuses (P = 0.001). The oral transit time, pharyngeal delay time and pharyngeal transit time did not show significant differences among the groups with swallowing of both thick and thin liquids. Penetration and aspiration were more frequent in the TPI group (P < 0.05) with swallowing of both thick and thin liquids. The results suggest that TAI is more related to oral phase dysfunction and TPI is more related to pharyngeal dysfunction. In ischemic stroke, patterns of swallowing difficulty may differ according to the vascular territory involved and this should be considered in the management of post-stroke dysphagia.