CD39 and CD73 are ecto-nucleotidases present on peripheral blood mononuclear cells (PBMCs) and play important roles in cancer progression by suppressing antitumour immunity. As such, CD39 and CD73 on PBMCs are emerging as immune signatures to predict disease outcomes and treatment responses in cancer patients. The current study aimed to examine the proportion of T and B cells, including CD39 and CD73 expressing subsets, by flow cytometry, in PBMCs isolated from 24 head and neck squamous cell carcinoma (HNSCC) patients prior to, during and following combination radiotherapy (radiotherapy with concurrent cisplatin chemotherapy and/or anti-epidermal growth factor receptor immunotherapy). Combination radiotherapy caused significant changes to T and B cells, including CD39 and CD73 expressing subsets. Sub-analysis of this cohort revealed no significant differences between concurrent chemotherapy (n = 6) or immunotherapy (n = 6). In contrast, PBMCs from human papillomavirus positive (HPV+) HNSCC patients (n = 16) displayed reduced pre-treatment proportions of CD73+ CD4+ T cells compared to PBMCs from human papillomavirus negative (HPV-) HNSCC patients (n = 7). The current study revealed that following combination radiotherapy, T and B cells, including CD39 and CD73 expressing subsets, undergo changes; Finally, results indicated that high and low pre-treatment proportions of CD73+ CD4+ T cells may provide an immune marker to identify the HPV status of HNSCC patients, respectively. This work forms part of a larger study using flow and mass cytometry to probe for potential immune signatures in this disease.