Adenomyoepithelioma (AME) of the breast and gastrointestinal stromal tumors (GISTs) are rare benign (primarily) tumors observed in the breast and gastrointestinal tract, respectively. The coexistence of both of these rare tumors is extremely rare; therefore, the author describes the clinical presentation and pathophysiological findings of such a unique case in this study. A 56-year-old female patient with no medical history presented with a substantial right breast lump, severe nausea, and vomiting, and suffered from iron deficiency anemia. Radiological observation and a right breast excisional biopsy diagnosed the patient with AME associated with ductal carcinoma in situ (DCIS). Endoscopy and a CT scan of the stomach revealed the existence of GIST. This is the first reported case of concurrence of a huge mass of AME and GIST in a patient. Histological and immunohistochemistry tests using p63, SMA, calponin, and Ki67 markers for the breast tumor and DOG-1, CD34, and CD117 markers for the gastric tumor revealed the non-invasive benign state. The patient had a right breast mastectomy with a negative resection margin. AME of the breast and GIST pose diagnostic challenges due to their erratic morphological characteristics and can cause misinterpretation drawn solely from radiological tests. Effective and accurate diagnostics require assessing the histological and immunohistochemistry findings of the tumor to identify the invasiveness of the neoplasm and the associated risk levels. This report, thus, creates awareness among clinicians and pathologists for the consideration of such possibilities and, therefore, conducts the necessary diagnostics and prophylactic treatments.