Gorham-Stout disease is a rare condition of uncertain aetiology characterised by lymphatic proliferation within osseous structures and subsequent massive osteolysis. This report describes the index case of a patient with multifocal Gorham-Stout disease involving the skull base with Chiari I malformation and recurrent aseptic meningitis without fistula. A five-year-old male presented following decompression of a Chiari I malformation with headaches, vomiting, and stiff neck and cerebrospinal fluid pleocytosis without growth of a pathogenic organism. Ongoing symptoms prompted a further three presentations over several months revealing persistent aseptic cerebrospinal fluid monocytic pleocytosis. Further investigation revealed multifocal osseous cystic disease and subsequent bone biopsy suggested Gorham-Stout disease. Suboccipital decompression was not repeated despite craniocervical junction re-stenosis. A literature review demonstrated the extreme rarity of Gorham-Stout disease associated with Chiari I malformation and meningitis. Potential mechanisms of these entities occurring in concert are discussed. Consideration of Gorham-Stout disease as a secondary cause for Chiari I malformation is important amid local bone changes or cerebrospinal fluid leakage prior to pursuing suboccipital decompression considering the poor outcomes reported.