Aims: programmed cell death ligand 1 (PD-L1) is the ligand of programmed death 1 (PD-1) which is a host immunity inhibitory receptor. PD-L1 expressed in tumor cells has been widely discussed, while there is little research about tumor intrinsic-PD-1. P-S6 is an important downstream effector of the PI3K/AKT/mTOR pathway. This study aimed to investigate the expression of PD-L1 protein and its relationship with cancer cell-intrinsic PD-1 protein and p-S6 in nasopharyngeal carcinoma (NPC). Methods: the expression of PD-L1, PD-1 and p-S6 proteins in tissues of NPC, non-cancerous nasopharyngeal epithelia, primary lesions and matching metastases was detected by immunohistochemistry. Results: PD-L1, PD-1 and p-S6 expression and co-expression of PD-L1 and PD-1 proteins were significantly higher in NPC than those of in the non-cancerous nasopharyngeal epithelia, respectively (all P<0.05). Furthermore, there was evidently elevated expression of PD-1 and co-expression of PD-L1 and PD-1 in matched metastasis of NPC compared to their primary lesions (all P<0.01). Overall survival rate for NPC patients with positive expression of PD-L1 (P =0.035) was significantly higher than others. Multivariate Cox proportional hazard regression analysis identified that positive expression of PD-L1 (P=0.002) and p-S6 (P=0.003) were independent prognostic factors for NPC patients. Conclusions: positive expression of PD-L1 associated with expression of cancer cell-intrinsic PD-1 and p-S6, PD-L1 might be a good prognostic biomarker and p-S6 could serve as a valuable independent poor prognostic biomarker for NPC patients.