Internal anatomical disorders in marine mammals often only become apparent during necropsies. A case of hemihydranencephaly (HHAE) in a harbor porpoise (Phocoena phocoena) is described herein. HHAE is a rare, severe congenital brain disorder whereby one cerebral hemisphere is replaced by a sac filled with cerebrospinal fluid. The harbor porpoise was a formerly stranded and rehabilitated juvenile female, exhibiting behavior during her life in captivity that fell into two distinct modes. During her normal, “active” mode, she behaved like other harbor porpoises and performed well in training sessions. During her abnormal, “passive” mode, she listed onto her left side and floated with her right side at the water surface for several minutes at a time. At least her right eye would be closed, and she appeared to be in deep sleep. While floating at the surface and tilted over, she probably occasionally inhaled small amounts of water, resulting in recurring pneumonia. Ten months after stranding, at the age of ~24 months, the porpoise suddenly died. She was diagnosed with right-sided HHAE upon necropsy, which suggests that her passive-mode behavior was abnormal sleep. Cetaceans exhibit unihemispheric sleep so that they can maintain voluntary breathing, swimming, thermoregulation, body position, and vigilance. Possessing only one cerebral hemisphere, the porpoise lost the ability to sleep in this way. Following necropsy, the proximate cause of her death was probably an extensive lung edema followed by hypoxia, but the HHAE was assumed to be the ultimate cause. This case report shows that, despite the negative outcome, HHAE in harbor porpoises can be compatible with life and may not result in the cognitive or motor impairments that are seen in some human HHAE patients.