Background <p>Neurological manifestations are sometimes seen in patients with multisystem inflammatory syndrome in children. Concurrent ataxia and papilledema are yet to be reported in patients with multisystem inflammatory syndrome in children.</p> Case presentation <p>A 13-year-old Iranian boy was transferred from a deprived area to the emergency department of Namazi Hospital (Shiraz, Iran) in May 2022 with fever, generalized skin rashes, palmar erythema, vomiting, and diarrhea. Severe conjunctivitis, photophobia, headache, and ataxia were also noted. His neurological manifestations improved following treatment with high-dose methylprednisolone and intravenous immunoglobulin. He was discharged 9 days later.</p> Conclusions <p>Physicians should be aware of ataxia and papilledema as extremely rare presentations of multisystem inflammatory syndrome in children.</p>