Purpose <p>FT-FAPI (FT, fast treatment) is a new FAP inhibitor with the potential to be used as a drug in boron neutron capture therapy (BNCT). The aim of this prospective study was to compare the diagnostic performance of ⁶⁸Ga-FT-FAPI and ⁶⁸Ga-FAPI-04 in patients with gastrointestinal (GI) tumors.</p> Methods <p>The study enrolled patients with histologically confirmed GI tumors diagnosed between March 2024 to April 2025 in Xijing Hospital. All the patients underwent paired ⁶⁸Ga-FT-FAPI PET/CT and ⁶⁸Ga-FAPI-04 PET/CT scans within three days. The maximum standard uptake value (SUVmax), tumor-to-background ratio (TBR), and retention index (RI) of the primary tumor and metastatic lesions were analyzed for both imaging modalities.</p> Results <p>A total of 19 patients with GI tumors (12 males and 7 females) with a median age of 61.3 years (range, 40–75 years) were finally enrolled in this study. A total of 186 lesions were identified.⁶⁸Ga-FT-FAPI identified all the tumors clearly with a higher uptake than ⁶⁸Ga-FAPI-04 (13.3 vs. 10.0, <i>P</i> &lt; 0.001), and better TBR (13.8 vs. 8.2, <i>P</i> &lt; 0.001). In terms of retention, the RIs of ⁶⁸Ga-FT-FAPI were significantly higher than those of ⁶⁸Ga-FAPI-04 for detecting lymph node metastases (88.7% vs. 76.2%, <i>P</i> = 0.001, <i>n</i> = 62), liver metastases (115.4% vs. 101.5%, <i>P</i> = 0.032, <i>n</i> = 38), bone metastases (70.8% vs. 57.0%, <i>P</i> = 0.008, <i>n</i> = 24), and peritoneal metastases (102.9% vs. 87.0%, <i>P</i> = 0.041, <i>n</i> = 26).</p> Conclusion <p>⁶⁸Ga-FT-FAPI had a superior performance than ⁶⁸Ga-FAPI-04 for uptake in lesions and a higher detection rate, especially for identifying metastases in lymph nodes, bone, liver and peritoneum. ⁶⁸Ga-FT-FAPI may therefore be an effective BNCT agent for diagnosis and treatment of GI tumors.</p>