This study aimed to analyze how the ubiquitin proteasome system (UPS) or autophagy lysosome system (autophagy) are induced in brain tissues at different intervals after traumatic intracranial injury in humans. Injured cerebral cortices of 36 forensic autopsy cases were analyzed by immunohistochemistry using antibodies as the UPS marker (ubiquitin and lysine 48-linked polyubiquitin chains [K48]) and autophagy marker (lysine 63-linked polyubiquitin chains [K63], p62/sequestome 1 and microtubule-associated protein 1 light chain 3 [LC3]). The number of neurons and glial cells with cytoplasmic inclusions that stained positive for ubiquitin, K48, and p62 began to increase within 1 hour after intracranial injury, particularly at contusion sites. From 3.5 hours onward, an increase in cytoplasmic inclusions that stained positive for K63 and LC3 began to be detected. LC3-positive cytoplasmic inclusions were not identified after 37 days; however, the increased immunoreactivity to ubiquitin and anti-K48 antibody was maintained for 7 months. These results suggest that the UPS is activated earlier and lasts longer than autophagy, that autophagy is activated for a relatively short term (between a few hours and approximately 1 month), and that the activation occurs especially in severely damaged brain tissues following head trauma in humans.