The effectiveness of PET-CT (positron emission tomography–computed tomography) was investigated for staging target delineation compared with CT-MR (computed tomography–magnetic resonance) and early response of intensity-modulated radiotherapy (IMRT). Gross tumour volume–clinical target volume (GTV-CTV) differences between PET-CT and CT-MR for 14 nasopharyngeal carcinoma (NPC) patients were compared. Evaluation of doses of organs at risk (OARs) was done by IMRT plans. Responses of IMRT were evaluated with both sets. PET-CT changed MR-based TNM (Tumour Lymph Nodes Metastasis) in 11 of 14 patients. The median GTVNP (nasopharyx gross tumour volume) was 49.25 and 18.8 cm3 for CT-MR and PET-CT, respectively. In eight cases, GTVNP in the PET-CT was smaller than the CT-MR. The PET-CT presented a larger GTVNP than the CT-MR for six cases. Mean doses for the parotid glands were found to be higher than in CT-MR-based plan in one patient although he had smaller GTVNP at the PET-CT. The median follow-up was 16 months. Only one patient experienced recurrence in the CTVNP (nasopharyx clinical target volume). MR showed a decrease in the size-number of lymph nodes in four patients whereas PET-CT showed no uptake. All patients had positive responses to IMRT in their second control MR and PET-CT. PET-CT could improve tumour delineation. This enables an increase in dose inside the CTV. PET-CT provided significant information on the control scans for most of our patients whose MR imaging showed residual or recurrence.