Background: Cholangiocarcinoma is a locally invasive, poorly treatable malignancy of the biliary tract that uncommonly metastasizes to the brain and rarely causes neuroophthalmologic complications. Case Presentation: A 34-year-old woman with an isolated sixth cranial nerve palsy underwent brain neuroimaging and was found to have a large sellar/suprasellar mass invading the cavernous sinus. Gross total resection was performed with improvement in the sixth cranial nerve nerve palsy. Next-generation sequencing and histology studies revealed an adenocarcinoma with a fibroblast growth factor receptor (FGFR)2-BICC1 gene mutation. Positron emission tomography/computed tomography scan demonstrated a large hypermetabolic partially necrotic hepatic mass with local invasion, and liver biopsy confirmed a diagnosis of cholangiocarcinoma. At three weeks after resection, the brain lesion recurred and the patient developed worsening diplopia. The patient then received stereotactic radiotherapy applied to the brain lesion and began treatment with gemcitabine and cisplatin. The patient was transitioned to FGFR-targeted therapy with pemigatinib, and the patient was alive at last follow-up, 49 weeks after diagnosis. Conclusion: To our knowledge, this is the first report of cholangiocarcinoma presenting as a neuro-ophthalmologic finding, consisting of an isolated sixth cranial nerve palsy, which was the harbinger of a brain metastatic sellar/suprasellar mass. The case highlights the importance of prompt neuroimaging in isolated cranial nerve palsies, particularly in younger patients, and consideration of rare aggressive metastasis to the sellar region, where prompt surgery and pathology are critical in identifying the primary carcinoma and to instituting expedited therapy.