Afatinib has improved the prognosis of epidermal growth factor receptor-positive advanced non-small cell lung cancer and has been explored in the treatment of human epidermal growth factor receptor 2 (HER2)-amplified breast cancer. However, its clinical efficacy in HER2-amplified endometrial cancer has not been reported. Herein, we present the clinical benefit of afatinib in a case of stage IIIC endometrioid adenocarcinoma refractory to multiple lines of chemotherapy and eventually developed pulmonary, abdominal and pelvic metastasis. Upon referral to our clinic, capture-based targeted sequencing was performed on both blood and tumor samples and revealed HER2 amplification. The patient was administered with afatinib and achieved partial response (PR) after two months of treatment, reflected by a significant reduction in pulmonary lesions and serum levels of tumor markers including carcinoembryonic antigen (CEA), cancer antigen (CA) 19-9, 125, 15-3 and cytokeratin 19 fragment antigen 21-1 (CY211). The patient passed away after 3 months of afatinib treatment due to suspected complications of severe intestinal obstruction. Our report demonstrates the efficacy of afatinib in a heavily pre-treated HER2-amplified endometrial cancer patient with multi-organ metastasis. This case also highlights the need to include comprehensive mutational profiling in the standard management of endometrial cancer patients for treatment guidance.