BACKGROUND The totally implantable venous access port (TIVAP) is an important device in patients for injecting blood products, parenteral nutrition or antineoplastic chemotherapy. Metastatic spread at the site of the insertion of a TIVAP is extremely rare. CASE SUMMARY We report the case of 33-year-old male with advanced gastrointestinal stromal tumor (GIST) who underwent radical tumor resection after neoadjuvant imatinib therapy. However, a solitary GIST metastasis at the site of a TIVAP insertion developed during adjuvant imatinib treatment. Mutational analysis showed secondary mutation in KIT exon 13 (V564A), which is resistant to imatinib treatment. To our knowledge, this is the first case report of a patient with advanced GIST developing GIST metastasis at the site of a TIVAP insertion. CONCLUSION This case highlights that when a patient with advanced, high metastatic GIST requires TIVAP insertion, we should realize that there is a risk of developing tumor metastasis at the site of a TIVAP insertion.