Purpose Pancreatic tumors are characterized by abundant desmoplasia including cancer-associated fibroblasts (CAFs) that express fibroblast activation protein (FAP). Gallium-68-labeled fibroblast-activating protein inhibitor (FAPI) is promising probe for positron emission tomography/computed tomography (PET/CT) imaging of various types of cancers. This work aims to compare the diagnostic performances of [68Ga]Ga-DOTA-FAPI-04 and [18F]FDG PET/CT in detecting primary pancreatic tumors and metastasis prospectively.Methods We collected patients with pancreatic tumors during May 1 to August 1, 2020. All the patients underwent [68Ga]Ga-DOTA-FAPI-04 and [18F]FDG PET/CT within 5 days at diagnosis, recurrence detection or therapeutic evaluation. The clinical information, PET/CT image characteristics, maximum standardized uptake (SUVmax) value of pancreatic tumors and metastases, target-to-background ratio (TBR) of the liver metastases were collected for analysis. The pathological results or follow-up clinical diagnostic results were obtained. Results A total of 45 patients (18 females and 27 males; median age of 62.4 years; range: 42 - 84 years) were enrolled for analysis, including 37 patients with pancreatic cancers and 8 patients with other types of pancreatic tumors. [68Ga]Ga-DOTA-FAPI-04 PET/CT detected abnormal pancreatic uptake in 36 patients (97.30%) with a SUVmax of 14.0 ± 5.4 (range 5.4 to 25.1), while 34 patients (91.89%) with abnormal pancreatic uptake with a SUVmax of 7.6 ± 3.9 (2.9 to 20.4) were detected by [18F]FDG PET/CT. Moreover, [68Ga]Ga-DOTA-FAPI-04 detected more lymph nodes (LNs) and metastases than [18F]FDG. The SUVmax of [68Ga]Ga-DOTA-FAPI-04 in LNs and TBR of liver metastases was higher than that of [18F]FDG (LNs: 6.1 ± 2.7 vs. 4.4 ± 1.6, TBR: 5.0 ± 3.1 vs. 2.9 ± 1.4 p < 0.0001), respectively. [68Ga]Ga-DOTA-FAPI-04 PET/CT successfully unregulated the clinical stage in 2 patients, visualized recurrence in 1 patient, and detected residual active tumor tissues in 2 patients with discordant imaging results (FAPI+/FDG-). In addition, there was nearly no [68Ga]Ga-DOTA-FAPI-04 or [18F]FDG uptake in pancreatic cystic neoplasms. Most of neuroendocrine neoplasms showed negligible [68Ga]Ga-DOTA-FAPI-04 uptake. Conclusion Compared with [18F]FDG PET/CT, [68Ga]Ga-DOTA-FAPI-04 PET/CT detected pancreatic tumors and associated metastases with a higher sensitivity and SUVmax value. However, false-positive uptake of [68Ga]Ga-DOTA-FAPI-04 in pancreatitis, cholangitis, some benign liver disease, and inflammatory LNs was also prominent.