Mesenchymal hamartoma of the liver (MHL) is an uncommon benign tumor found primarily in children younger than 2 years of age. We report a rare case of MHL with a daughter nodule and atypical histological findings in a 14-month-old girl. On admission, computed tomography, magnetic resonance imaging, and angiography showed a solid hypovascular mass with a central cystic area in the liver. Laparotomy revealed a tumor, 8 cm in size, occupying segment 5 and parts of segments 4 and 6 of the liver, and a small nodule, 10 mm in size, in segment 7. Thus, we performed a partial hepatic resection (S4-6) and tumor extirpation (S7). The histological findings of both tumors were the same, but atypical of MHL. Recent studies on the pathogenesis of this tumor have found neoplastic features such as genetic anomalies and malignant transformation. These findings suggest that the conventional approach of completely resecting the tumor whenever possible is the best treatment.