Background: In adults, Baker's cyst development is attributable principally to secondary alterations after degenerative changes. The latter changes often accompany osteoarthritis, and we frequently encounter patients with Baker's cysts seeking total knee arthroplasty (TKA). Baker's cysts are not usually subject to extensive preoperative evaluation because the cysts often disappear naturally after surgery, unaccompanied by any adverse symptoms. Case presentation: A 63-year-old woman presented with moderate pain in the left knee joint that had developed 1 year ago. Posterior knee pain was aggravated on maximum knee flexion. Three months previously, a popliteal mass had become palpable and the patient had undergone needle mass aspiration twice in a local orthopedic hospital, but the mass had recurred. We initially considered TKA for her severe degenerative osteoarthritis. However, we decided to perform only arthroscopic debridement and cyst excision because the patient was experienced severe pain only on maximal knee flexion, and did not want TKA. Pus gushed from the torn cyst during the operation. We diagnosed an infected Baker's cyst. The patient was treated with a first-generation cephalosporin postoperatively. Conclusions: A Baker's cyst that was aspirated and still causes symptoms with altered blood tests needs to be evaluated accurately before TKA.