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Abstract Background As a common disease in orthopedic clinics, popliteal cysts often coexist with intra-articular lesions. Compared with traditional open surgery, arthroscopic treatment of popliteal cysts is less traumatic, and intra-articular lesions can be treated. The ‘one-way valve’ mechanism of the popliteal cyst can be removed by expanding the communication between the articular cavity and the cyst to avoid cyst recurrence. In terms of arthroscopic techniques, the comparison of clinical effects between the double posteromedial portal (DPP) and single posteromedial portal (SPP) has rarely been studied. The purpose of this retrospective study was to compare the clinical effects of DPP and SPP. Methods A total of 46 consecutive patients with symptomatic popliteal cysts who underwent arthroscopic treatment were included in this study and followed for approximately 1 year. All patients were divided into two groups according to the arthroscopic portals (DPP group and SPP group). The cyst size, Lysholm score and Rauschening–Lindgren (R–L) grade were evaluated before the operation for all patients, and the intra-articular lesions, operative time and complications were recorded after operation. At the last follow-up, the Lysholm score and R–L grade were recorded, and magnetic resonance imaging was used to evaluate the outcome of the cyst. The clinical data of the two groups was statistically compared and analyzed. Results There were no significant differences in preoperative cyst size, Lysholm score or R–L grade between the two groups (P > 0.05). The operation time of the DPP group (67.52 ± 18.23 min) was longer than that of the SPP group (55.95 ± 16.40 min) (P = 0.030), but the recurrence rate of cysts in the DPP group (0%) was obviously lower than that in the SPP group (19.0%) (P = 0.046). There were no significant differences in the Lysholm score, R–L grade or complication rate between the two groups at the last follow-up (P > 0.05). Conclusion Arthroscopic treatment of popliteal cysts using double posteromedial portals was a safe and effective surgical method. Trial registration: ChiCTR, ChiCTR2200060115. Registered 19 May 2022, https://www.chictr.org.cn/showproj.html?proj=133199