The majority of gastrointestinal stromal tumors (GISTs) arise in the stomach and small intestine; primary GIST of the liver is extremely rare. GISTs share specific immunohistological features with melanoma, therefore, determining a definitive diagnosis can be difficult. However, electron microscopy can be used to aid the differential diagnosis of GIST. The present study reports the first case of a KIT/platelet‑derived growth factor receptor α (PDGFRA) wild‑type, primary GIST arising from the liver in a long‑term survivor of anorectal melanoma. The patient underwent APR for treatment of malignant melanoma of the anorectum in 2001 with no adjuvant therapy and remained disease-free until 2009. In 2009, the patient presented with a solitary, rapidly growing hypervascular liver tumor, which was subsequently diagnosed as a primary GIST of the liver. Imatinib treatment (400 mg/day) was initially administered for two months, however, disease progression occurred. Therefore, the patient underwent chemotherapy with doxorubicin (50 mg/m2) and cisplatin (50 mg/m2) every three weeks. Although this temporarily resulted in stable disease, progression occurred five months later. Finally, oral sunitinib (37.5 mg/day) was administered; however, the patient succumbed to the disease one month later. Despite the current GIST patient exhibiting a poor response to imatinib, the present study highlights the importance of considering a second primary malignancy and performing immunohistochemical analysis upon the occurrence of a newly developed lesions in long‑term remission cancer survivors.