Periodontitis and chronic kidney disease are both chronic inflammatory diseases and share some common risk factors. This 3-month pilot study aimed to clarify whether non-surgical periodontal therapy is beneficial in clinical, biochemical, and microbiological conditions in patients with periodontitis and kidney failure. Kidney failure patients with moderate to severe periodontitis were recruited from two hospitals. Treatment group received non-surgical periodontal therapy, and control group received oral hygiene instruction only. Outcome assessments were conducted 1 and 3 months after treatment. Non-parametric tests were used to analyze the patient-level data. Periodontal site-level assessments were analyzed by Student -test and paired -test. Statistical significance was set at -value < 0.05. A total of 11 subjects completed the study. There was no significant difference between groups in all-cause mortality, cardiovascular events, infection events, systemic parameters, and serum biomarkers. Comparing to control group, clinical periodontal parameters, gingival crevicular fluid interleukin-1β (IL-1β) level and periodontal pathogens showed significant improvement in the treatment group. Non-surgical periodontal treatment did not change systemic outcomes in kidney failure patients, but changed the local micro-environment.