BACKGROUND This retrospective study of 42 patients with popliteal cysts (or Baker cysts) aimed to compare the effects on duration and outcomes of arthroscopic surgical debridement with and without the use of cyst injection with methylene blue (MB). MATERIAL AND METHODS Medical records of patients who underwent conventional arthroscopic surgery (n=20) or arthroscopic surgery after MB injection (n=22) for popliteal cysts between 2018 and 2021 were reviewed. The MB group underwent arthroscopic popliteal cystectomy with MB as the marker, and the control group underwent conventional arthroscopic popliteal cystectomy. Surgical time of cyst resection, postoperative bruising extent, complication rate, and cyst recurrence rate of the 2 groups were compared. RESULTS The MB group had a faster surgical cyst removal time (16.5±1.5 min) than the control group (24.5±1.6 min; P<0.05). The MB group had less postoperative bruising (1 case, 4.5%) than the control group (5 cases, 25%; P<0.05). The surgical results were similar in both groups, with a Lysholm score of 87.23±1.80 in the MB group and 87.23±1.62 (P>0.05) in the control group. CONCLUSIONS This study showed that preoperative injection of MB for popliteal cysts before arthroscopic debridement improved cyst localization and ease and accuracy of surgery and reduced operative time, adjacent tissue damage, postoperative complications, and recurrence rate.