The boy, who has not been named, was given the vaccine when he was 18 months old, and was diagnosed with Severe Combined Immunodeficiency Disease (SCID) four months later.
Over the following months, he was treated with drugs to treat symptoms of fever, rash, diarrhoea, lethargy and seizures. MRI scans detected encephalitis, or brain inflammation caused by infection.
The symptoms worsened, and by the time he was four, he was uncoordinated and was losing his sight.
Further tests discovered damage to the central nervous system and chronic inflammation, but despite being given antibiotics, antivirals and antifungal drugs, he died when he was five, by which time he was blind.
In post mortem examinations, researchers at University College London found a virus strain that came from the MMR in the boy's brain.
Lead researcher Sofia Morfopoulou says the boy may have had an impaired immune system before he was vaccinated, which made him more susceptible to a severe reaction. A similar case happened in 2015 when a 13-month-old girl died from encephalitis after being given the MMR.