18F-fluorodeoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT) plays an important role in locating of primary tumor for patients with head and neck cancer of unknown primary (HNCUP). Nevertheless, it can be challenging to locate the primary malignancy in 18F-FDG-PET/CT scan in some cases. As 68Ga-radiolabeled fibroblast activation protein inhibitor (FAPI) PET/CT has promising results in detecting different tumor entities, our study aimed to evaluate the performance of 68Ga-FAPI-PET/CT for detecting the primary tumor in HNCUP patients with negative 18F-FDG findings. Methods: A total of eighteen patients (16 males and 2 females; median age, 55 years; range, 24-72 years) with negative 18F-FDG findings were enrolled in this study. All patients underwent 18F-FDG and 68Ga-FAPI-PET/CT within one week. Biopsy and histopathological examinations were done in the sites with positive 68Ga-FAPI-PET/CT findings. Results:68Ga-FAPI-PET/CT detected the primary tumor in 7 out of 18 patients (38.89%). Among the 7 patients, in respect of the primary tumor sites, 1 was in nasopharynx, 2 were in palatine tonsil, 2 were in submandibular gland, and 2 were in hypopharynx. The primary tumors showed moderate to intensive uptake of FAPI (mean SUVmax, 8.79; range, 2.60-16.50) and excellent tumor-to-contralateral normal tissue ratio (mean SUVmax ratio, 4.50; range, 2.17-8.21). In lesion-based analysis, a total of 65 lymph nodes and 17 bone metastatic lesions were identified. The mean SUVmax of lymph node metastases were 9.05 ± 5.29 for FDG and 9.08 ± 4.69 for FAPI (P = 0.975); as for bone metastases, the mean SUVmax were 8.11 ± 3.00 for FDG and 6.96 ± 5.87 for FAPI, respectively (P = 0.478). The mean tumor-to-background ratio (TBR) values of lymph node and bone metastases were 10.65 ± 6.59 vs. 12.80 ± 8.11 (P = 0.100) and 9.08 ± 3.35 vs. 9.14 ± 8.40 (P = 0.976), respectively. Conclusion: We presented first evidence of diagnostic role of 68Ga-FAPI-PET/CT in HNCUP, and our study demonstrated that 68Ga-FAPI-PET/CT had the potential to improve the detection rate of primary tumor in HNCUP patients with negative FDG findings. Moreover, 68Ga-FAPI had similar performance in assessing metastases with 18F-FDG.