Because lymphocyte telomere length (LTL) plays critical roles in the maintenance of genomic stability and integrity, LTL thus may influence the etiology and prognosis of squamous cell carcinoma of the oropharynx (SCCOP). However, given the association between LTL and risk of human papillomavirus (HPV)-associated SCCOP and between LTL and tumor HPV status of SCCOP, we hypothesized that LTL is associated with SCCOP prognosis, particularly in HPV-positive patients after definitive radiotherapy. LTL and tumor HPV type 16 (HPV16) status were determined in 564 incident SCCOP patients before radiotherapy or chemoradiation. Both univariate and multivariable Cox regression analyses were performed to estimate the association between LTL and prognosis. Eighty-five percent patients had HPV16-positive tumors. Patients with shorter telomeres had significantly better overall, disease-specific and disease-free survival than did those with longer telomeres (log-rank P < 0.001). Moreover, patients with shorter telomeres had significantly lower risk of death overall [hazard ratio (HR) = 0.2; 95% confidence interval (CI) = 0.1-0.4], death due to SCCOP (HR = 0.2; 95% CI = 0.1-0.4) and SCCOP recurrence (HR = 0.3; 95% CI = 0.2-0.5) after adjusting for other important prognostic confounders. Finally, we found more pronounced effects of LTL on survival in HPV16-positive SCCOP patients after stratified analysis according to tumor HPV status. These findings indicate that LTL plays a significant role in the survival of patients with SCCOP, especially HPV16-positive patients who undergo definitive radiotherapy. Therefore, pretreatment LTL may be an independent prognostic biomarker for HPV16-positive SCCOP. Prospective studies with larger sample sizes are needed to confirm these findings.