Acute encephalopathy is a syndrome characterized by an acute onset of disturbance of consciousness. Many acute encephalopathies are caused by viral infections; however, they can also be a result of bacterial infections. Acute focal bacterial nephritis (AFBN) can cause neurological symptoms, such as irritation, unconsciousness, and seizures. In some cases, AFBN-associated acute encephalopathy has also been reported. This report describes the first case of acute encephalopathy without the characteristic findings of MRI-associated AFBN. The patient was a 3-year-old male, who had febrile seizure at the ages of 1 and 2 years. He developed disturbance of consciousness, irritability, excitability, and neck stiffness on the day after admission. There were no abnormal findings on brain MRI; however, a generalized high-voltage slow wave was noted on electroencephalography (EEG). His urinary sediment count was elevated, and Morganella morganii and Enterococcus faecalis were detected in the urinary culture. A diagnosis of acute encephalopathy with urinary tract infection (UTI) was made.