Background While Covid-19 predominantly affects the respiratory system, neurological manifestations including encephalitis occur in some patients, possibly affecting the course and outcome of the disease. Here, we describe a unique case of a young man with Covid-19 and transient MOG-positive encephalitis, with a benign course. Case presentation A 22-year-old male, with PCR confirmed Covid-19 infection was admitted because of persistent headache. The clinical examination was normal. Neuropsychological testing revealed distinct executive deficits. Brain MRI and cerebrospinal fluid (CSF) analysis were suggestive for encephalitis. Further laboratory examination revealed a serum MOG antibody titre. The headache improved with analgetic treatment and i.v. methylprednisolone. Consequently, the MOG antibody titer decreased and MRI lesions were resolving. The patient made a full recovery, with no signs of deterioration over the following months. Conclusions Covid-19 manifestations in the CNS include encephalitis with variable course and prognosis. This case highlights a possible association between inflammation due to COVID-19 and transient secondary autoimmunity with transient MOG antibodies and atypical clinical presentation.