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Background A two-stage prosthesis exchange procedure has been the gold standard in surgical treatment of the chronically infected knee arthroplasty so far. This includes 2 surgeries/hospitalizations and an interim period of 2–3 months between surgeries with impaired health, functional status and quality of life of the patients. A one-stage exchange procedure holds many obvious advantages compared to the two-stage approach, but outcomes of a one-stage versus two-stage procedures have never been investigated in a randomized clinical trial. The purpose of this study is primarily to investigate time-adjusted differences in functional status of patients after one-stage versus two-stage revision. Secondary, to report time-adjusted differences in quality of life, complications (including re-revisions due to infection) and mortality. Methods This study is a pragmatic, multi-center, randomized, non-inferiority trial comparing one-stage versus two-stage revision of the infected knee arthroplasty. Seven Danish hospitals are currently participating in the study, but additional hospitals can enter the study if adhering to protocol. Ninety-six patients will be included prospectively. Follow-up will be with PROM-questionnaires and clinical controls up to 10 years. The patients who are not able to participate in the randomized trial are followed in a parallel cohort study. PROM’s Oxford Knee Score and EQ5D + EQ5D VAS questionnaires are completed preoperatively and sent out to the study participants at 6 weeks, 3, 6, 9, 12, 18 and 24 months as well as 5 and 10 years postoperatively. In addition a tailor made cost questionnaire on the non-treating hospital resource use, community health and social service use, travel costs, time off work and informal care are sent out. Discussion If one of the two treatment alternatives is found superior in both domains of quality of life (both knee-specific and generic) and health economics, that treatment should be promoted. Other outcomes will open informed discussions about treatment strategies for periprosthetic knee infections. Trial registration The randomized trial is registered on ClinicalTrials.gov with ID NCT03435679, initial release date January 31, 2018 and the cohort study is registered with ID NCT04427943, submitted January 8, 2020 and posted June 11, 2020.