We assessed the role of [18F]FDG-PET/CT in identifying and managing cancer of unknown primary site (CUP syndrome). We reviewed [18F]FDG-PET/CT scans of individuals with CUP syndrome recorded in clinical referral letters from 2012 to 2019. We evaluated the identification of primary tumor (PT) by [18F]FDG-PET/CT, according to histological subtype, and the impact on clinical management. The median age was 65 years, 36/64 males (56%). PTs were detected in 28/64 (44%) patients. Detection was significantly lower in patients with squamous cell carcinoma (SCC) than with other histologies combined, p = 0.034. Mean age, mean SUVmax (10.6 ± 6.0) and organ involvement were similar between patients with and without discovered PTs; and between patients with SCC and with other histologies combined. However, those with SCC were less likely than the others to present with multi-lesion involvement, p < 0.001. [18F]FDG-PET/CT interpretations apparently affected treatment of 8/28 (29%) patients with PT detected, and in none of the 35 whose PT was not discovered, p < 0.001. [18F]FDG-PET/CT appeared helpful in detecting PT in almost half the patients with CUP syndrome; the lowest rate was for patients with SCC pathology. PET/CT showed limited overall value in guiding clinical management, however benefited those with discovered PT.