Unexpected extraosseous uptake is common on Tc-methylene diphosphonate bone scintigraphy, but accumulation by primary upper gastrointestinal tract malignant melanoma is rarely reported. The present case is a 58-year-old woman with a 10-day history of diffuse bone pain and weakness. Her bone scintigraphy showed unexpected diffuse gastric tracer uptake. Subsequent gastroscopy revealed a number of hyperpigmented lesions in the stomach and duodenal bulb. Malignant melanoma was confirmed by histopathology and immunohistochemistry. Because extensive physical examination failed to identify any other site of ocular and cutaneous melanoma, a diagnosis of primary upper gastrointestinal tract malignant melanoma was established.