Small cell carcinoma (SCC) is a neuroendocrine tumor (NET) commonly found in the lung, known for rapid proliferation and early metastasis. Extrapulmonary small cell carcinomas (ESCC) are rare, with GI tract carcinomas exceedingly so. Due to the lack of clinical data on the treatment of ESCC, the standard regimen is the same as the SCC of the lung. Documented accounts of paraneoplastic encephalomyelitis associated with NETs are also uncommon. We present a patient who suffered from neurologic deficits before being diagnosed with paraneoplastic encephalomyelitis from a duodenal ESCC. The patient presented with ear pain and hematemesis. New symptoms arose after the resolution of initial symptoms, including shortness of breath and numbness. Autoimmune workup was positive for anti-Hu antibodies. A position emission tomography (PET) scan showed increased uptake in the duodenal region. Biopsy results from a duodenal ulcer revealed poorly differentiated neuroendocrine carcinoma with positive synaptophysin and strong positivity of Ki-67, consistent with ESCC. Numerous treatments, including platinum-based chemotherapy, yielded no neurologic improvement for the patient. This case details an atypical presentation of ESCC, which should be considered in patients suspected of paraneoplastic encephalomyelitis.