Gastrointestinal stromal tumors (GISTs) are mesenchymal tumors accounting for only a small fraction of all primary malignant tumors of the gastrointestinal tract. Histologically, GISTs are classified as epithelioid, spindle type, or mixed. We present a case of a 66-year-old male incidentally noted to have a pedunculated gastric mass along the lesser curvature of the stomach during a laparoscopic Nissen fundoplication and hiatal hernia repair. A wedge resection was performed and the pathology demonstrated a 3.7 cm GIST of epithelioid type. Four years after the initial surgery, a jejunal mass was identified via CT enterography as part of a workup for ongoing iron deficiency anemia. A laparoscopic small bowel resection was performed, and the pathology revealed a new primary 3.2 cm GIST of the spindle cell subtype. Three years after surgery, surveillance imaging is negative for any recurrence. This appears to be the first report of the occurrence of metachronous primary GISTs of different histologic subtypes, separated by location.