Radiolabelled fibroblast activation protein inhibitor (FAPI) tracers have the potential to overcome the limitations of 2-deoxy-2-[¹⁸F]fluoro-D-glucose ([¹⁸F]FDG) and improve the diagnosis and staging of hepato-pancreato-biliary (HPB) cancers. This study aims to compare the diagnostic performance of radiolabelled FAPI versus [¹⁸F]FDG PET imaging in HPB cancers. A systematic search of PubMed, Embase, Web of Science and Cochrane Library was performed to identify eligible studies on the diagnostic performance of FAPI PET for primary HPB tumours (hepatocellular carcinoma (HCC), pancreatic cancer (PC) and biliary tract cancer (BTC)) and for liver metastases of gastrointestinal origin. The diagnostic performance was defined as a combination of detection rate and semi-quantitative tracer uptake. A random-effects model was used to calculate the risk differences. In total, 28 studies were included. Histopathology was the reference standard for the primary tumour in 26 studies (93%). The detection rate of radiolabelled FAPI in comparison to [¹⁸F]FDG was significantly higher in HCC (0.33, 95% CI: 0.20–0.47 and 0.34, 95% CI: 0.23–0.45) and BTC (0.27, 95% CI: 0.11–0.43 and 0.28, 95% CI: 0.08–0.48), in the patient- and lesion-based analyses, respectively. In PC, no differences were observed. Radiolabelled FAPI outperformed [¹⁸F]FDG in the lesion-based detection of lymph node, liver and extra-hepatic metastases. In all HPB cancers, the mean SUVmax was significantly higher with radiolabelled FAPI compared to [¹⁸F]FDG. Molecular imaging with FAPI PET seems to have several benefits over [¹⁸F]FDG PET in HPB cancer diagnostics, with an overall higher tracer uptake, and higher detection rates in HCC and BTC.