Neuroendocrine tumor (NET) is a deadly malignancy disease that can be found anywhere in the body. The lack of tumor‐specific treatment led to the worse prognosis of NET. Anaplastic lymphoma kinase‐tyrosine kinase inhibitors (ALK‐TKIs), such as alectinib and crizotinib, have been used in the treatment of NET patients with ALK rearrangement. However, the response to ensatinib in NET patients with rare ALK fusion has been rarely reported. Here, we report a 55‐year‐old Chinese female patient with NET (atypical carcinoid tumor) and a novel CEP44‐ALK rearrangement identified by next‐generation sequencing (NGS). NGS can provide more information on mutation landscape for rare neuroendocrine tumors to guide treatment and assist in clinical decisions by presenting molecular changes. The patient received ensartinib (225 mg/day) for 18 months until disease progression in June 2024 and achieved a radiographic partial response. Although patients with ALK fusions showed response to ensatinib in nonsmall cell lung cancer (NSCLC), this study first reports a metastatic NET case with a novel CEP44‐ALK rearrangement that responded favorably to ensartinib.