Background: Patients with nasopharyngeal carcinoma (NPC) who have hepatitis B virus (HBV) infection tend to be treated with induction chemotherapy (IC) due to a higher metastasis rate. However, additional IC may lead to immunosuppression and can negatively affect the prognosis. We evaluated whether receiving IC improved the prognosis of patients with NPC co-infected with HBV, on the basis of concurrent chemoradiotherapy (CCRT).Methods: This large-scale retrospective cohort study included data of patients with pathologically confirmed NPC that were collected from two hospitals between January 2010 and March 2014. Patients were followed-up every 3 months during the first 2 years and once every 6 months thereafter. Univariate analysis identified confounding factors associated with prognosis. Stage-based subgroup analyses and 1:1 random-matched pair analyses were performed to compare the survival differences between patients treated with IC + CCRT and those treated with CCRT alone.Results: Among the 1,076 enrolled patients, 16.6% were hepatitis B surface antigen (HBsAg)-positive.Among HBsAg-positive patients with stage II/III/IV NPC, distant metastasis-free survival (DMFS) (79.3% vs. 89.9%; P=0.045) and progression-free survival (PFS) (70.6% vs. 83.7%; P=0.025) were lower in patients who received IC + CCRT than in those who received CCRT alone. After adjusting for confounding factors, IC + CCRT was validated as a negative prognosticator for DMFS and PFS, while matched-pair analysis with HBsAg-negative patients showed a better overall survival (OS) for IC + CCRT (88.4% vs. 82.6%; P=0.04).Conclusions: Compared with CCRT alone, IC + CCRT negatively affects DMFS and PFS in patients with NPC with chronic HBV infection. We advocate withholding IC but administering stronger initial treatment in NPC patients complicated with HBV infection.