Systemic mastocytosis is a rare disease resulting from infiltration of atypical mast cells in multiple organ systems and present with variety of symptoms. Primary appendiceal and cecal mass with isolated abdominal pain as a presenting feature in systemic mastocytosis have not been reported in literature up to now. We described a 69- years-old female with systemic mastocytosis who presented with chronic abdominal pain and recent progression. On imaging of the abdomen and pelvis showed a mass in cecum. The patient underwent surgery and histopathologic evaluation of cecal and appendiceal masses revealed uniform small round cell tumor with eosinophilic cytoplasm admixed with many eosinophils distorting normal colonic mucosal architecture. The neoplastic cells showed positive expression of CD117 and Mast cell tryptase. According to all these considerations systemic mastocytosis was confirmed as the diagnosis. Isolated abdominal pain and primary large intestinal mass are uncommon features of systemic mastocytosis. This case report informed physicians and pathologists to consider it as one of differential diagnosis.