Auto-immune N-methyl-D-aspartate receptor encephalitis (NMDARE) is a relatively recently described cause of acute encephalopathy with very few reports from sub-Saharan Africa (SSA). We report a case of NMDARE in a young Kenyan female who was transferred to our facility with headaches, insomnia, behaviour changes and latterly pathognomonic orofacial dyskinesias. We comprehensively ruled out infectious and other inflammatory/auto-immune causes. She was diagnosed with NMDARE by positive antibody testing in serum and cerebrospinal fluid and changes on brain magnetic resonance imaging. She was immunosuppressed with high-dose steroids, intravenous immunoglobulins, plasma exchange and rituximab, and showed signs of neurological improvement clinically and radiologically. Unfortunately, she succumbed to septic shock from prolonged intensive care. This is the first report of NMDARE in an indigenous patient from the eastern SSA. The majority (>80%) of patients are either left with mild disability or make a full recovery after NMDARE, but some factors - which comprise the NMDARE One-Year Functional Status (NEOS) prognostication score - can adversely affect outcome, as was the case in our patient.