Gallium-68-labeled fibroblast activating protein inhibitor (68Ga-FAPI) has been developed for positron emission tomography (PET) and proved to be a promising imaging agent. It has shown good diagnostic performance in the diagnosis of various solid tumors, including head and neck cancers (HNC). This study conducted a meta-analysis on the diagnostic performance of fluorine-18-fluorodeoxyglucose (18F-FDG) and 68Ga-FAPI in HNC, summarized the clinical evidence of 68Ga-FAPI for HNC, and compared the diagnostic sensitivity of the two imaging agents in the primary and metastatic lesions of HNC. PubMed/ Medline, Embase and Cochrane Library databases were searched from built to 31 January 2023. Studies on patients with HNC underwent paired 18F-FDG and 68Ga-FAPI were included. Literature screening, full text review and data extraction were performed by 2 investigators. The risk of bias was examined with the QUADAS-2 tool. Meta-analysis of diagnostic test sensitivity was performed by a random-effect model and displayed by a forest plot. A total of 507 studies were comprehensively retrieved, and 11 studies, 297 patients were selected for the systematic review and 9 studies for meta-analysis. Two hundred and nine patients selected for initial staging and 88 patients for recurrence. Pooled sensitivity at initial stage was conducted. Based on primary lesions, the sensitivity were 18F-FDG 0.95 (0.81-0.99) vs 68Ga-FAPI 0.99 (0.90-1.00). For lymph node metastases, based on patients, the sensitivity were 18F-FDG 0.99 (0.77-1.00) vs 68Ga-FAPI 0.92 (0.68-0.98); For distant metastases, based on patients, the sensitivity were 18F-FDG 0.82 (0.03-1.00) vs 68Ga-FAPI 0.92 (0.59-0.99). Gallium-68-FAPI has great potential in the diagnosis of HNC and has similar diagnostic value with 18F-FDG. While there is much overlap in the performance (as measured by sensitivity) of these two agents but a trend may favor 68Ga-FAPI over 18F-FDG for detection of primary tumor and distant metastases. Therefore, in the diagnosis and evaluation of head and neck cancers, the combination of 68Ga-FAPI and 18F-FDG can be considered according to the individual situation.