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A branchial cleft cyst (BCC) is a neck mass, present from birth, caused by incomplete development of the branchial arches during fetal development. It commonly presents as a solitary, painless mass in the neck of a child or young adult. We present a case of a large intramedullary BCC in a patient with Klippel-Feil syndrome (KFS). A male in his 60s presented with long-lasting neck pain and fast-progressing paraparesis. MRI showed a large intramedullary cystic tumour in the cervicothoracic spine with accompanying cervical diastematomyelia and extensive cervical vertebrae fusion. The patient was operated on from a posterior approach with C6-Th2 laminectomy with neuromonitoring. Gross total resection was achieved. The postoperative period was without complications, and after 3 months, the patient made a full recovery. Based on histopathological examination, a BCC was diagnosed.