Background: The chemokine network orchestrates the cancer stem-like property and consequently participates in cancer progression. CXCR3 contributes cancer progressive property and immunomodulation in the tumor microenvironment. The two major isoforms of CXCR3 are scrutinized and the divergence is showed that CXCR3A promotes cancer cell growth and motility while CXCR3B functions contrarily in many studies. However, rare studies illustrate the role of CXCR3 isoforms in cancer stem-like property and chemoresistance, especially in head and neck cancer (HNC). Methods: Levels of CXCR3, CXCR3B, and Sox2 were determined in HNC tissue microarray by immunohistochemistry staining to explore potential clinical relevance. Lentivirus-mediated CXCR3-isoform overexpression with MTS assay, clonogenic assay, transwell migration, sphere formation, and chemo-drug susceptibility were implemented to investigate the role of CXCR3-isofoms in HNC. Results: High levels of CXCR3 were significantly associated with advanced stage (p < 0.01), regional lymph node metastasis (p < 0.05), and poor differentiation (p < 0.005) and further correlated with worse survival rate in oral cancer patients (p = 0.036). Higher levels of CXCR3B were found in regional lymphatic invasion of HNC and progressive stage of squamous cell carcinoma. Elevated Sox2 expression was significantly associated with the advanced stage of HNC in the oral cavity, and demonstrated a co-expression pattern with CXCR3B. Furthermore, lentivirus-mediated overexpression of CXCR3A and CXCR3B in SAS human oral cancer cells promoted cell mobility. CXCR3A overexpression enhanced sphere-forming ability and chemoresistance of CSCs by upregulating stemness-related genes. Conclusion: This study first provides a novel insight of CXCR3 isoform A in HNC cancer progression via regulating cancer stem-like properties and chemoresistance, suggesting that CXCR3A may be a prognostic marker and novel target for HNC therapy.