We report on a 15-year-old girl with severe anti-N-methyl-D-aspartate receptor encephalitis who had initial poor prognostic factors. We delineate the unique challenges faced in the rehabilitation of our patient including sleep disruption and food aversion. After 20 months of hospitalization and intensive rehabilitation, there was a significant improvement in functional abilities and self-care skills. However, she had residual neurocognitive deficits, visual perceptual, and motor coordination difficulties that continued to improve after discharge, attesting to the need for long-term rehabilitation. The case showed the need for a coordinated multidisciplinary approach, with both targeted therapies and neuropharmacology, tailored to facilitate the different stages of recovery unique to anti-N-methyl-D-aspartate receptor encephalitis patients.