Gastrointestinal stromal tumors (GIST) are a rare and unique group of mesenchymal tumors arising from the gastrointestinal tract, omentum, mesentery, and retroperitoneum. Though they have certain typical radiological features that can differentiate them from epithelial tumors, it is often difficult to differentiate them from other non-epithelial tumors. Their features also vary depending on their size, site of origin, etc. When differentiation from other mesenchymal tumors on histopathology is difficult, receptor tyrosine kinase (C-KIT proto-oncogene/CD117) and gastrointestinal stromal tumor (GIST-1) discovered on GIST1 (DOG-1) expression are confirmatory. The concurrent presence of other primary cancers with GISTs has been described in the literature, among which most have been of gastrointestinal origin. Few cases of primary breast cancer in GIST have been described. Lymph nodal metastasis is rarely encountered in GIST, and metastasis to the breast is even rarer. We present a case of a 39-year-old female with non-specific symptoms who was referred for ultrasonography (USG) and computed tomography (CT) that showed a small intestinal GIST along with a breast lump and axillary lymphadenopathy that were labeled as metastases from the GIST on frozen sections; however, they were later diagnosed as primary breast cancer with axillary metastases on the histopathology and immunohistochemistry of the excision biopsy specimens post-surgery. The patient underwent surgical resection and chemotherapy.