To study the effects of concomitant subchondral bone cysts (SBCs) on prognosis after arthroscopic bone marrow stimulation (BMS) for osteochondral lesions of the talus (OLTs) less than 100 mm2 and to further assess the correlation between cystic OLT area, depth, or volume and postoperative outcomes. We retrospectively analyzed consecutive patients with OLTs (<100 mm2) who received BMS between April 2017 and May 2020 with a minimum follow-up of 24 months. Lesion area, depth, and volume were collected on preoperative magnetic resonance imaging. Visual analog scale (VAS), American Orthopedic Foot and Ankle Society, Karlsson-Peterson, Tegner, Foot and Ankle Ability Measure (FAAM)-Activities of Daily Life and Sports scores were assessed before surgery and at the latest follow-up. Additionally, a general linear model (GLM) and a Pearson correlation analysis (PCA) were performed to investigate the effects of concomitant cysts on postoperative results. Eighty-two patients with a mean follow-up of 39.22 ± 12.53 months were divided into non-cyst (n= 45; 39.91 ± 13.03 months) and cyst (n= 37; 38.37 ± 12.02 months) groups. There was no significant difference in the OLT area between the non-cyst and cyst groups (46.98 ± 19.95 mm2 vs 56.08 ± 22.92 mm2; P= .093), but the cyst group showed significantly greater depth (6.06 ± 1.99 mm vs 3.96 ± 1.44 mm; P= .000) and volume (248.26 ± 156.81 mm3 vs 134.58 ± 89.68 mm3; P= .002). The non-cyst group showed significantly more improvement in VAS pain, Karlsson-Peterson, Tegner, and FAAM scores than the cyst group (P < .05). The GLM indicated that SBCs negatively affected VAS pain and Tegner scores (P < .05). For OLTs with cysts, the PCA showed that an area of 90.91 mm2, depth of 7.56 mm, and volume of 428.13 mm3 were potential cutoff values associated with poor outcomes. The concomitant SBCs negatively affected the prognosis of OLTs after BMS. For OLTs with cysts, an area of 90.91 mm2, depth of 7.56 mm, and volume of 428.13 mm3 were the potential cutoff values associated with poor outcomes after BMS. Level III, retrospective comparative study.