Background: Osteoarthritis is a destructive joint disease that leads to degeneration of cartilage and other morphological changes in the joint. No medical treatment currently exists that can reverse these morphological changes. Intra-articular injection with autologous, micro-fragmented adipose tissue has been suggested to relieve symptoms. Methods/Design: The study is a blinded randomized controlled trial with patients allocated in a 1:1 ratio to 2 parallel groups. Patients suffering from pain and functional impairment due to osteoarthritis Kellgren-Lawrence grades 2–3 in the tibiofemoral joint are eligible for inclusion. The intervention group is treated with an intra-articular injection with autologous, micro-fragmented adipose tissue prepared using the Lipogems® system. The control group receives an intra-articular injection with isotonic saline. In total, 120 patients are to be included. The primary outcome is The Knee injury and Osteoarthritis Outcome Score (KOOS4) evaluated at 6 months. Secondary outcomes are KOOS at 3, 12 and 24 months; the Tegner activity score; treatment failure; and work status of the patient. The analysis will be conducted both as intention-to-treat and per-protocol analysis. Discussion: This trial is the first to investigate the efficacy of autologous, micro-fragmented adipose tissue in a randomized controlled trial. The study uses the patient-reported outcome measure Knee Injury and Osteoarthritis Outcome Score (KOOS4) after 6 months as the primary outcome, as it is believed to be a valid measure to assess the patient’s opinion about their knee and associated problems when suffering from osteoarthritis.