Objective End-stage kidney disease (ESKD) patients have a higher risk of antibiotic-associated encephalopathy (AAE) than other patients. We aimed to evaluate the prevalence, risk factors and outcomes of AAE in ESKD patients. Method A retrospective study of ESKD patients treated with intravenous antibiotics in our hospital from Jan. 1, 2006, to Dec. 31, 2015 was performed. AAE was diagnosed by the modified Delphi method. Control individuals were randomly selected from the remaining patients who did not exhibit neurologic symptoms. Logistic regression analysis was used to identify risk factors for AAE as well as the association between AAE and outcome. Result A total of 2104 patients were included in the study. The prevalence of AAE in our study was 4.4% (92/2104). The multivariate logistic regression analysis revealed that anuria (OR = 8.04, 95% CI: 4.13-15.65, p < 0.001), history of central nervous system disorder (OR = 3.03, 95% CI: 1.21-7.56, p = 0.018) and hypoalbuminemia (OR= 1.87, 95% CI: 1.01-3.47, p = 0.046) were independent factors associated with AAE in ESKD patients. After adjustment for confounders, AAE was associated with composite outcomes of in-hospital mortality and treatment withdrawal (OR = 4.36, 95% CI: 2.09-9.10, p < 0.001). Conclusion The prevalence of AAE was 4.4% in ESKD patients and varied among different antibiotics. Anuria, history of central nervous system disorder and hypoalbuminemia were associated with AAE in ESKD patients. AAE is associated with worse outcomes in ESKD patients.