Objective. The 5-year clinical outcomes and prognostic factors of nasopharyngeal carcinoma (NPC) patients treated with intensity modulated radiotherapy (IMRT) were evaluated. Methods. Six hundred ninety five NPC patients primarily treated with IMRT in Sichuan Cancer Hospital from January, 2003 to December, 2006 were analyzed retrospectively, including 540 males and 155 females. The prescription dose was delivered as follows: gross target volume (GTVnx) 67-76 Gy in 30-33 fractions, positive neck lymph nodes (GTVln-R/L) 60-70 Gy in 30-33 fractions, high-risk clinical target volume (CTV1) 60-66 Gy, low-risk clinical target volume (CTV2) 54-60 Gy, and clinical target volume of cervical lymph node regions (CTVln) 50-55 Gy. Results. The 5-year local control (LC), regional control, distant metastasis-free survival (DMFS), disease free survival, disease specific survival, and overall survival (OS) rates were 89.8%, 95.2%, 74.1%, 69.6%, 83.2%, and 77.1%. The 5-year DMFS of IMRT and IMRT combined with chemotherapy was 62.1% and 70.9%, the OS of them was 72.9% and 79.1%. The incidence of grade 3 acute and late toxicity was 38.3% and 4.2%, respectively. Conclusion. The 5-year LC and OS rate of NPC treated with IMRT was 89.8% and 77.1%. The clinical stage, N stage, volume of GTVnx, and chemotherapy were the main prognostic factor for the OS. Distant metastasis was the main pattern of failure.