Encephalomalacia is the softening or loss of brain tissue after cerebral infarction, cerebral ischemia, infection, craniocerebral trauma, or other injury. The term is usually used during gross pathologic inspection to describe blurred cortical margins and decreased consistency of brain tissue after infarction. Multicystic encephalomalacia refers to the formation of multiple cystic cavities of various sizes in the cerebral cortex of neonates and infants after injury, most notably perinatal hypoxic-ischemic events. Chronic sinusitis has become one of the most common diseases in otolaryngology practice. Many of these patients can be managed successfully with medical therapy. Those who fail intensive medical therapy may be candidates for functional endoscopic sinus surgery (ESS). This procedure has variable complication rates and can have some serious consequences. Serious complications of functional ESS are very rare, but cerebrospinal fluid leak, meningitis, hemorrhage, infection, or vision loss has been reported in a few cases. In this study, we present a 57-year-old man with encephalomalacia after a penetrating brain injury incurred during ESS.