Background In Indonesia, nasopharyngeal carcinoma (NPC), a malignancy of the head and neck, has a high mortality rate because patients are usually diagnosed at an advance stage and, in some, metastasis has even occured. When diagnosed at an early stage, 5-year survival rates can reach more than 80%, but at advance stages, 5-year survival rate is only 10–40%. Epstein-Barr virus is associated with the pathogenesis of NPC. These viral-induced carcinoma express the stress surface protein molecules MHC class I-related chain A (MICA), part of an important activation pathway to trigger the immune system to attack tumour cells. However, the virus and cancer cells might downregulate the expression of membrane-bound MICA (mMICA) molecules and increase the soluble MICA (sMICA) concentration, therefore reducing the immunogenicity of the tumour cell and decreasing the prognosis. We aimed to determine the concentration of sMICA as prognostic factor in NPC. Methods We used immunohistochemical analysis to determine mMICA and ELISA to determine sMICA concentration from the sera. We used Kruskal–Wallis and Mann–Whitney test for analysis. Findings mMICA expression was present in all NPC tissue (100%) in various concentrations. Mean sMICA concentrations was 245.8 pg/dL in NPC stage II, 369.9 pg/mL in stage III, and 464.8 pg/mL in NPC stage IV. The higher the sMICA concentration, the higher the NPC stage. There was no significant difference in sMICA concentration between stage III and stage IV NPC (p = 0.344). Interpretation Increased concentration of sMICA protein is a prognostic factor in NPC.