A 3-year-old girl underwent a surgery at an external center on July 2011 for a swelling in the left lumbar paravertebral subcutaneous region. The mass was completely excised and the pathologic diagnosis was a yolk sac tumor (YST). Laboratory tests revealed a serum α-fetoprotein level of 278 IU/mL. Investigations using bone scintigraphy and magnetic resonance imaging revealed a scar tissue at the surgical site and lesions indicating metastasis at the lumbar first, second, third, and fifth vertebra. The patient was administered 5 cycles of PEB (cisplatin, etoposide, bleomycin) treatment. The serum α-fetoprotein was 3 IU/mL after the treatment. The lumbar magnetic resonance imaging and bone scintigraphy results were normal. The patient continues to be in remission since June 2012. YSTs are most commonly seen in the testis, ovary, and sacrococcygeal regions. Atypical locations have been reported with the primary lesion in the stomach, diaphragm, omentum, sino-nasal region, cranial base, lungs, vagina, and penis. Our case is probably a YST with an atypical location derived from preliminary cells left under the skin because of a migration defect.