Gastrointestinal stromal tumors are the most common primary mesenchymal tumors of the gastrointestinal tract accounting for 0.1%-3.0% of all gastrointestinal malignancies. The stomach is the most common site (60%) followed by the small bowel (30%-35%) particularly jejunum and ileum, colorectum (5%) and rarely affect esophagus and appendix. Most gastrointestinal stromal tumors arise sporadically, however, less commonly they develop in association with various clinical syndromes like Carney triad, Carney-Stratakis syndrome, familial gastrointestinal stromal tumor syndrome and neurofibromatosis type1 (NF1). We report a 65-year-old male patient presented with gastric mass (7.5 × 4.5 × 3.5 cm) arising from the posterior gastric wall. Histologic examination revealed neoplastic proliferation of spindled and epithelioid cells with focal plexiform pattern and low mitotic activity 3/50 HPF. No evidence of cytological atypia, abnormal mitosis or necrosis. Interestingly enough, there were focal areas of mature bone formation/osseous differentiation associated with calcification. The tumor cells were strongly positive for CD117, DOG1 with focal immunoreactivity against CD34. The morphologic features and the immunoprofile were diagnostic of gastrointestinal stromal tumor. Herein, we present a rare case of gastric gastrointestinal stromal tumor with mature bone formation, osseous metaplasia and calcification. To the best of our knowledge, this is the second case report of gastric gastrointestinal stromal tumor with osseous differentiation and mature bone formation.