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Abstract Background Cavernous sinus thrombosis (CST) is a very rare disease and can occur as a result of pharyngitis, a face infection, sinusitis, orbital cellulitis, otitis, traumatic injury, or surgery, particularly if the patient has a thrombophilic disease. So far, no myelodysplastic syndrome (MDS) cases with CST have been recorded. We describe a case of CST induced by Covid-19 in a patient with MDS. Case presentation A 71-year-old woman with MDS was admitted to the hospital due to headache, weakness, diplopia, and drooping of the left eyelid. Pancytopenia was found. Left cavernous sinus thrombosis and encephalitis were also confirmed by Magnetic resonance imaging (MRI). A thorax Computed Tomography (CT) revealed bilateral patchy ground-glass opacities consistent with Covid-19. The patient was treated with low molecular weight heparin and discharged with partial recovery. Conclusions It's important to remember that CST can occur in people with Covid-19 infection, even if they have severe thrombocytopenia like MDS.