This case report documents an extremely rare presentation of primary uterine yolk sac tumour (YST) in a premenopausal woman in her late 40s, who presented with heavy menstrual bleeding. Imaging was suggestive of a uterine tumour with rising serum germ cell markers. In the absence of preoperative histology, a surgical staging was performed, confirming pathological diagnosis and immunohistochemistry (SALL4 and alpha-fetoprotein (AFP) positive). She received adjuvant chemotherapy as per protocol. With a short disease-free interval, she had a rise in serum AFP with recurrence in the lungs, which was successfully treated with second-line chemotherapy. This case uniquely highlights the importance of comprehensive tumour marker assessment, the role of marker-guided surveillance in early relapse detection, and demonstrates the feasibility of successful salvage therapy. The case expands current knowledge of extragonadal YST management, encourages vigilance for atypical presentations and underscores the value of individualised multimodality care—even in aggressive, relapsed disease—for achieving complete remission.