Cancer of unknown primary (CUP) is a common diagnosis in adult oncology, but is extremely rare in pediatrics, with few published reports and none in the era of molecular profiling. Here, we describe a 13-year old boy with metastatic adenocarcinoma of unknown primary that was refractory to conventional chemotherapy. Molecular profiling revealed an activating ERBB2 D769Y variant. He subsequently achieved disease control on a lapatinib-containing regimen, and upon progression, he transiently responded to neratinib prior to dying from disease. Our case reports a rare example of pediatric CUP and highlights the utility of molecular profiling in these cases.