Chondromyxoid fibroma (CMF) is a rare benign bone tumour, constituting less than 1% of all primary bone tumours and typically affects long bones. It is an even rarer presentation in the head and neck region and can prove diagnostically challenging. We report a case of a 43-year-old woman diagnosed with a left-sided skull base CMF, an atypical location for this tumour. The patient presented with progressive palatal pain without any orbital symptoms. Imaging, including magnetic resonance imaging (MRI), revealed a well-circumscribed lesion centred in the pterygopalatine fossa, extending into the orbit toward the superior orbital fissure. An excisional biopsy demonstrated features consistent with CMF. Surgical resection was subsequently performed via an endoscopic transnasal approach, and follow-up imaging at six months showed no signs of recurrence. In addition to the case presentation, we reviewed the existing literature on head and neck CMF cases, focusing on clinical presentation, treatment options, and long-term outcomes. While CMF is rare in this region, careful diagnostic and surgical management is crucial due to the potential for misdiagnosis and recurrence. This case demonstrates the benefits of minimally invasive endoscopic surgery, allowing for complete tumour removal with minimal morbidity. Our report highlights the role of endoscopic approaches in the treatment of skull base and orbital CMF and contributes to the growing body of literature on the management of CMF in the head and neck region.