A gastrointestinal stromal tumor (GIST) is a mesenchymal neoplasm of the gastrointestinal tract often known to express c-KIT or platelet-derived growth factor receptor alpha (PDGFRα). Among all GI tract cancers, they account for less than 1% of cases. Most patients become symptomatic in the later stages of the tumor's course, often presenting with insidious anemia due to gastrointestinal bleeding and metastasis. The recommended management of solitary GIST is surgery, while larger or metastatic tumors that express c-KIT are managed with imatinib as either neoadjuvant or adjuvant therapy. Due to the progression of these tumors, they are at times associated with systemic anaerobic infection, which is an indication of malignancy workup. In this case report, we discuss a 35-year-old woman who was discovered to have GIST with possible hepatic metastasis complicated by pyogenic liver disease due to Streptococcus intermedius and the diagnostic challenge of differentiating between infection and tumor.