To evaluate long-term outcomes and late toxicities of nasopharyngeal carcinoma (NPC) patients with T1-2N0-3M0 stage in intensity-modulated radiotherapy (IMRT) era. From June 2005 to October 2013, 276 patients confirmed T1-2N0-3M0 NPC treated with IMRT were reviewed, with 143 (51.8%) N0-1 disease and 133 (48.2%) N2-3 disease. Among them, 76.4% received chemotherapy. The prescribed doses given to the primary tumor and lymph nodes were 66Gy in 30 fractions. After a median follow-up of 103 months, the 5-year and 10-year overall survival (OS) were 90.6% and 79.2%. The 5-year and 10-year local control (LC) rate, regional control (RC) rate and distant metastasis free survival (DMFS) were 97.0% and 91.9%, 94.1% and 92.2%, 89.4% and 87.0%, respectively. The 5-year and 10-year OS, RC rate and DMFS of N0-1 compared with those of N2-3 were 98.6% vs. 82.0% and 86.8% vs. 70.9% (P=0.000), 99.3% vs. 88.3% and 99.3% vs. 84.1% (P=0.000), 97.9% vs. 80.1% and 95.7% vs. 77.5% (P=0.000). The incidence of 3-4 late toxicities were low and mainly xerostomia and hearing deficit. The rates of radiation-induced cranial nerve palsy and temporal necrosis were 2.5% and 2.5%, respectively. Eighteen patients had the second primary tumor, of whom eight were lung cancer, six were head and neck cancer, four were others. Satisfactory locoregional control was achieved in T1-2N0-3M0 NPC treated with IMRT. Distant metastasis was the main failure cause and N2-3 was the main adverse prognostic factor. Second primary tumor occurred 6.5% and negatively impacted OS in NPC.