[18F]FDG PET/CT to detect unknown primary lesions is essential for clinical management but still has limitations. [68Ga]Ga-FAPI is a tumor-stromal imaging agent that provides a promising alternative to [18F]FDG for the assessment of malignancies. We aimed to investigate whether [68Ga]Ga-FAPI PET/CT has an additional role in identifying unknown primary lesions with negative or equivocal [18F] FDG PET/CT results.This single-center prospective clinical study was conducted between March 2020 and March 2022 at Southwest Medical University Hospital. Patients underwent [18F]FDG PET/CT for the identification of unknown primary lesions. They underwent repeat [68Ga]Ga-FAPI PET/CT when [18F]FDG PET/CT results were negative or equivocal. Histopathological examination, surgery, or clinical follow-up (at least 3 months) for FAPI-positive lesions. The diagnostic efficacy of [68Ga]Ga-FAPI in identifying unknown primary lesions was evaluated.A total of 44 participants (median age, 57 ± 12 [SD]; 22 [50%] men) were evaluated. Thirteen of the 44 patients had equivocal [18F]FDG PET/CT findings, while the diagnosis was clear on [68Ga]Ga-FAPI PET/CT. [68Ga]Ga-FAPI PET/CT also revealed primary lesions in additional 17 patients with negative [18F]FDG PET/CT findings. In fourteen of 44 patients, no primary lesion was detected by either tracer. On this basis, we analyzed 94 lymph node metastatic lesions. The mean SUVmax of lymph node metastases on [68Ga] Ga-FAPI PET/CT and [18F]FDG PET/CT were 9.2 ± 5.1, 7.9 ± 4.8 (p = 0.03) and the mean TBR were 9.1 ± 5.2, 4.9 ± 3.1 (p < 0.01), respectively.[68Ga]Ga-FAPI PET/CT showed great potential for identifying unknown primary lesions and has the potential to improve the detection rate of unknown primary lesions with negative or equivocal for [18F]FDG findings.ClinicalTrial.gov. Identifier: ChiCTR2100044131.© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.