Meckel’s diverticulum is one of the representative diseases that causes melena in childhood. 99mTc scintigram is performed for a definitive diagnosis. However, we still encounter false-negative cases. We report a case of Meckel’s diverticulum in a 3-year-old girl in which abdominal ultrasonography findings served as diagnostic clues for the operation, despite the negative findings of 99mTc scintigram. She visited our hospital with vomiting and melena. We found a low echoic intraabdominal mass like a target sign approximately 11 mm in size with rich blood flow. In addition, she had blueberry-like melena after enema. Therefore, we considered Meckel’s diverticulum. However, 99mTc scintigram was negative. We performed surgery because the ultrasonographic findings did not change. We found an invagination caused by Meckel’s diverticulum. This case demonstrates that it is possible to make a diagnosis of Meckel’s diverticulum with abdominal ultrasonography even if 99mTc scintigram is negative.