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Background: Associated joint disorders with popliteal cysts were stated approximately between the ranges of 41-83 % in all reported cases. Combined treatment strategies that eliminate intra-articular pathologies and cyst- associated valve mechanisms are thought to be a good option in treatment of the disease. In this study, our main objective is to present clinical results of our combined treatment results, which includes posterior cyst excision with supine arthroscopic intervention, targeting intra-articular pathologies on recalcitrant cases. Methods: One hundred three knees of 100 patients treated with posterior open cystectomy with valve and repair of posterior capsule, in addition to arthroscopic treatment of intra-articular lesions, were included in the study. Preoperative magnetic resonance imaging (MRI) studies were performed in order to evaluate location of Baker cysts behind the knee. Rauschning-Lindgren and Lysholm Knee Scoring Scales were used to assess pre/post-operative knee functions. Mann-Whitney U test was used to evaluate the differences between genders in comparison of Lysholm and Lindgren scores. Mean age within gender groups was compared using independent samples t-test. Wilcoxon test was used to compare the change in Lysholm and Lindgren scores. A p-value of less than 0.05 was considered to show a statistically significant result. Over the 1-year follow-up period, US and MR imaging was performed only with symptomatic patients. Results: Cyst recurrence was seen only in 2 (1.94 %) patients. Post-operative Lysholm Knee and Lindgren knee scores demonstrated improvement in knee function and general comfort level of the patients. Conclusions: Our midterm follow-up (Mean: 39 Months) results showed that open cyst excision with valve and capsule repair with knee arthroscopy that targets associated intra-articular pathologies reduced the pain and improved the knee function in those patients. Level of evidence: IV (Retrospective clinical study without comparison group). [ABSTRACT FROM AUTHOR]