Intracranial empyema is a rare but serious complication of sinusitis in children. Myelodysplastic/myeloproliferative syndromes (MMS), including juvenile myelomonocytic leukemia (JMML), can lead to immunosuppression, thus favouring infections. We report the case of a sphenoid sinogenic retro-clival extradural empyema in a 14-year-old female patient associated with JMML. Treatment consisted in an endonasal transphenoidal drainage of the empyema associated with intravenous antibiotherapy. The patient was thereafter enrolled in chemotherapeutic treatment with Azacitidine. The disease progressed to blast phase, indicating bone marrow graft. This is the first reported case of an endocranial complication of bacterial sinusitis associated with MMS in a child.