PurposeTo conduct a head-to-head comparison of the diagnostic ability of 68Ga-DOTA-FAPI-04 (68Ga-FAPI) and 18F-FDG PET/MR in nasopharyngeal carcinoma (NPC) patients.MethodsPatients diagnosed with NPC were prospectively enrolled. All patients underwent head-and-neck 68Ga-FAPI PET/MR and 18F-FDG PET/MR within one week. Primary tumor, lymph node numbers, and tracer uptake were compared by SUVmax and visual evaluation. The primary tumor volumes derived from 68Ga-FAPI, 18F-FDG PET, and MRI were also compared.ResultsFifteen patients were enrolled from June to August 2020. Both 68Ga-FAPI and 18F-FDG PET had 100% detection rate of the primary tumor. The 68Ga-FAPI SUVmax of primary tumors (13.87±5.13) was lower than that of 18F-FDG (17.73±6.84), but the difference was not significant (p=0.078). Compared with 18F-FDG, 68Ga-FAPI PET improved the delineation of skull-base invasion in eight out of eight patients and intracranial invasion in four out of four patients. When 25%SUVmax of 68Ga-FAPI or 20%SUVmax of 18F-FDG was utilized as a threshold for determining tumor volume, it was highly consistent with MRI. 18F-FDG PET detected much more positive lymph nodes than 68Ga-FAPI (100 vs 48). The SUVmax of 48 paired lymph nodes was significantly lower on 68Ga-FAPI than 18F-FDG (8.67±3.88 vs 11.79±6.17, p<0.001). Additionally, 68Ga-FAPI further detected four highly suspected small, distant metastases in three patients. Compared with 18F-FDG, 68Ga-FAPI changed overall staging in six of fifteen patients, with three patients being up-staged, and three down-staged.Conclusion68Ga-FAPI outperforms 18F-FDG in delineating the primary tumor and detecting suspected distant metastases, particularly in the evaluation of skull-base and intracranial invasion, suggesting 68Ga-FAPI hybrid PET/MR has the potential to serve as a single-step staging modality for patients with NPC. However, its value regarding lymph node and distant metastases evaluation needs further study.Trial registration: NCT04554719. Registered September 8, 2020 - retrospectively registered, http://clinicaltrails.gov/show/ NCT04554719