Sepsis-associated encephalopathy (SAE) is common and has poor clinical outcome. Sepsis increases autophagy in the brain. This study was designed to determine the role of autophagy on SAE including the brain structures related to learning and memory and the effects of pyrrolidine dithiocarbamate (PDTC), an anti-inflammatory agent, on autophagy and SAE. Six- to eight-week old CD-1 male mice were subjected to cecal ligation and puncture (CLP). Some mice received intracerebroventricular injection of the autophagy suppressor 3-methyladenine (3-MA) or intraperitoneal injection of PDTC immediately at the completion of the CLP. ELISA was used to measure interleukin (IL)-1β, IL-6, IL-10, and tumor necrosis factor α. Autophagy-related protein expression in the cerebral cortex and hippocampus was analyzed by Western blotting. The cognitive functions of mice were analyzed by Barnes maze and fear conditioning tests. CLP increased microtubuleassociated protein light chain 3 II (LC3II) and Beclin 1 and decreased p62 in the brain. CLP also increased proinflammatory cytokines and impaired learning and memory. These effects were inhibited by 3-MA and PDTC. Spine proliferation and maturation were impaired by CLP, which was attenuated by PDTC and 3MA. Abundant autophagic vacuoles were observed by transmission electron microscopy in CLP group. LC3II immunostaining was co-localized with that of ionized calcium-binding adapter molecule 1 and microtubule-associated protein-2. The co-staining was attenuated by 3-MA and PDTC. Our results suggest that sepsis increases autophagy in the microglia and neurons. Inhibiting autophagy improves SAE and brain structures related to learning and memory in mice. Autophagy and inflammation in the brain may regulate each other during sepsis.