Several epidemiological studies suggest that long-term survivors of acute kidney injury (AKI) have an increased risk of cognitive dysfunction, including dementia. Recent research has identified kidney-gut crosstalk mediated by immune function in AKI. Furthermore, the gut dysbiosis, which refers to the disruption of the gut microenvironment, has emerged as a significant complication of AKI. We hypothesize that alleviating gut dysbiosis with probiotics may help mitigate cognitive dysfunction following AKI. Using a mouse long-term AKI survival model (one year after kidney ischemia-reperfusion injury (IRI)), subjects were divided into two groups: one group received phosphate-buffered saline for control, while the other was administered probiotics. Functional and structural brain alterations were assessed one year post-IRI via behavioral tests (Y maze test) and immunohistochemistry analysis. One year after kidney IRI, spontaneous alternation, which reflects short-term memory and cognitive function, was assessed using the Y maze test. In both the sham and IRI groups, the probiotics-treated group tended to show improved cognitive function compared to the non-treated group. Furthermore, in the IRI group, probiotics administration significantly alleviated the decline in spontaneous alternation. In immunohistochemistry analysis, no significant differences were identified among groups. This study suggests that oral administration of probiotics may represent a potential strategy for preventing and treating long-term cognitive dysfunction in AKI.