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Myoepithelioma-like tumor of the vulvar region (MELTVR) is a rare mesenchymal subcutaneous tumor of low malignant potential that occurs in adult women and has typical histological features, including loss of SMARCB1 (INI1) expression. This report describes the case of a 23-year-old woman with a painful vulvar subcutaneous nodule and a diagnosis of MELTVR and describes the challenges in the approach to definitive diagnosis. A 23-year-old woman presented with a three-month history of right pubic pain. Imaging revealed a 25-mm inguinal lesion without metastasis. Biopsy demonstrated spindle and plasmacytoid tumor cells in myxoid and hypercellular areas, suggesting myoepithelioma. Although necrosis and mitotic activity were not evaluable in the biopsy specimen, malignant potential could not be excluded. Complete surgical excision was subsequently performed. The resected tumor measured 45 × 35 × 15 mm and showed multilocular solid and gelatinous areas. Histologically, lobulated growth, marked atypia, necrosis, and mitotic activity (9/10 HPF) were identified. Immunohistochemically, tumor cells showed positivity for estrogen receptor (ER) and progesterone receptor (PgR), along with loss of SMARCB1 (INI1) expression. Other markers, such as neural and myoepithelial markers, were negative. Fluorescence in situ hybridization (FISH) analysis showed no Ewing sarcoma breakpoint region 1 (EWSR1) rearrangement. MELTVR was diagnosed based on integrated clinicopathological and molecular findings. Biopsy specimens may fail to capture key diagnostic features of MELTVR because of intratumoral heterogeneity. Definitive diagnosis requires comprehensive evaluation of resection specimens with immunohistochemical and molecular analyses. This case may contribute to establishing diagnostic criteria for this rare entity.