Objective: The aim of the study was to investigate clinical evidence for defining the indications of prophylactic level IB radiotherapy (RT) in nasopharyngeal carcinoma (NPC). Methods: We conducted a phase 2 prospective study in 116 newly diagnosed patients with NPC treated by intensity-modulated RT. Whether level IB was irradiated is based on the risk score model (RSM). Two groups based on RSM were obtained: low risk and high risk. Omission of level IB irradiation was conducted in the low-risk group, otherwise level IB was contoured as part of the treatment target. Grade 2 or worse xerostomia at 12 months was assessed by the European Organization for Research and Treatment of Cancer (EORTC) QLQ-H&N35 questionnaire. Results: At a median follow-up of 16 months (range, 1–26 months), none of the patients developed failures at level IB. The 1-year overall survival, locoregional recurrence-free survival, and distant metastasis-free survival rates were 98.3%, 97.2%, and 95.8%, respectively. At 12 months xerostomia side-effects were reported in 90 of 116 alive patients; grade 2 or worse xerostomia at 12 months was significantly lower in the low-risk group than in the high-risk group. Conclusion: Omission of level IB irradiation was feasible for patients with low-risk IB lymph nodes metastasis.