Cell-free scaffolds used in cartilage regeneration are produced from different materials. The aim of this study is to compare the clinical and radiological results of two different scaffolds with hyaluronan- or chitosan-based structure used in the treatment of symptomatic condylar osteochondral lesions. The study comprises 69 patients who were operated for osteochondral lesion repair with hyaluronan- (n = 37) or chitosan-based (n = 32) scaffold. The International Knee Documentation Committee (IKDC), Lysholm Knee Scoring Scale and Visual Analog Scale (VAS) scores were collected for both groups at the preoperative and postoperative 3rd, 12th, and 24th months. Magnetic resonance imaging was performed between the 12th and 15th months postoperatively and this with magnetic resonance observation of cartilage repair tissue (MOCART) scoring were compared. Within group assessments demonstrate significant improvement in IKDC, Lysholm, and VAS scores at postoperative 3rd and 12th months. However, in both groups, IKDC, Lysholm and, VAS scores at the postoperative 24th month indicate no significant further improvement, compared with the 12th month results. There was no significant difference between the groups in terms of IKDC, Lysholm, VAS, and MOCART scores at any time period. This study shows that both scaffolds are useful in cartilage regeneration but have no clinical or radiological superiority to each other. Surgeons should select the method with which they feel comfortable. This is a level III, retrospective comparative study.