Purpose To compare the clinical outcomes and toxicities of two-dimensional conventional radiotherapy (2D-CRT) and intensity-modulated radiotherapy (IMRT) for the treatment of children and adolescent nasopharyngeal carcinoma (NPC). Methods A total of 176 children with non-metastatic NPC treated at Sun Yat-sen University Cancer Center between October 2003 and September 2013 were included in this study. Of the 176 patients, 74 received 2D-CRT and 102 were treated with IMRT. The clinical outcomes and acute and late toxicities were determined and compared. Results The IMRT group achieved significantly higher overall survival (OS) (90.4% vs. 76.1% at 5 year, P = 0.007) and disease-free survival (DFS) (85.7% vs. 71.2%, P = 0.029) mainly due to an improvement in locoregional relapse-free survival (LRRFS) (97.9 vs. 88.3%, P = 0.049). After stratification by disease stage, IMRT provided significant benefits for patients with stage III-IV disease in terms of OS, LRRFS and DFS. Multivariate analyses indicated that the treatment group (2D-CRT vs. IMRT) was a prognostic factor for OS, LRRFS and DFS. A significant reduction in Grade 2-4 xerostomia (52.7 vs. 34.3%, P = 0.015) and hearing loss (40.5 vs. 22.5%, P = 0.010) was observed in patients treated by IMRT. Conclusion IMRT provides better locoregional relapse-free survival and overall survival, especially in late-stage children and adolescent NPC patients, and is associated with a lower incidence of Grade 2-4 xerostomia as well as hearing loss compared with 2D-CRT. Distant metastasis remains a challenge in the treatment of children and adolescent NPC.