Purpose The study aimed to compare the diagnostic accuracy of Ga-68-DOTA-FAPI-04 (Ga-68-FAPI) and F-18-FDG PET/CT for peritoneal carcinomatosis (PC) in patients with various types of cancer. Methods The study enrolled 113 patients with suspected peritoneal malignancy, each of whom underwent Ga-68-FAPI and F-18-FDG PET/CT scans. Lesions in all patients were confirmed through pathology or radiological follow-up. The evaluation and comparison of diagnostic performance, visual scores, maximum standardized uptake value (SUVmax), mean tumor-to-background ratio (TBR), and the peritoneal cancer index (PCI) score were conducted. Results Compared to F-18-FDG, Ga-68-FAPI PET/CT presented higher sensitivity, negative predictive value, and accuracy for detecting PC on a patient-level (100% vs. 93.2%, 100% vs. 22.22% and 93.81% vs. 86.73%, respectively). Semi-quantitative evaluation revealed that Ga-68-FAPI PET/CT had significantly higher SUVmax and TBR for PC [(6.06 +/- 3.04 vs. 4.82 +/- 2.75, P = 0.001) and (8.50 +/- 5.01 vs. 2.92 +/- 1.67, P < 0.001)]. The PCI-FAPI score for PC was higher than the PCI-FDG score (11.28 +/- 7.10 vs. 5.69 +/- 5.15, P < 0.001). Conclusions Ga-68-FAPI has demonstrated superior diagnostic accuracy compared to F-18-FDG PET/CT in detecting PC with various types of cancer, particularly gastric cancer. Additionally, Ga-68-FAPI has shown significantly higher uptake and PCI score in PC compared to F-18-FDG, indicating its potential importance in clinical.