In this study, the potential advantage of FAPI over 18 F-labelled deoxyglucose ( 18 F-FDG) in evaluation of the initial staging colorectal cancer (CRC) was investigated. Thirty-two patients with histopathologically confirmed primary CRC were included in our study. They all underwent both 18 F-FDG and FAPI PET/CT. Lesion detectability and tracer uptakes, mainly quantified by maximum standardized uptake value (SUVmax) and target-to-background ratio (TBR), were compared for paired lesions between both modalities using the Wilcoxon signed-rank test and paired t-test. Thirty-five CRC lesions in 32 patients were diagnosed. The sensitivity of FAPI PET/CT in diagnosis of the CRC lesions was 100% while 93.8% of 18 F-FDG PET/CT. FAPI and 18 F-FDG had a similar uptake in CRC lesion (mean SUVmax: 14.3 ± 8.6 vs. 15.4 ± 9.8, P = 0.604), but lesions contained mucus and/or signet-ring cell carcinoma seemed to have a trend of higher FAPI uptake although there was no statistical difference (mean SUVmax: 12.7 ± 5.6 vs. 8.5 ± 4.1, P = 0.152) and higher TBR (13.4 ± 6.2 vs. 4.9 ± 2.2, P = 0.004) than those of 18 F-FDG. For regional lymph node metastases, both FAPI and FDG PET/CTs showed high sensitivity (7/8 vs. 7/8), specificity (7/8 vs. 6/8) and accuracy (14/16 vs. 13/16) (all P > 0.05). For distant metastasis, FAPI PET/CT depicted more positive lesions in distant lymph node (46 vs. 26), liver (13 vs. 7) and peritoneum (107 vs. 45) than 18 F-FDG PET/CT. FAPI PET/CT also had a higher peritoneal cancer index score (median 11 vs 4; P < 0.001) than 18 F-FDG PET/CT in evaluation of peritoneal metastases. FAPI PET/CT showed high sensitivity in detection of primary CRC and superiority to 18 F-FDG PET/CT in detection of metastases to distant lymph node, liver and peritoneum.