Background Matrix-induced autologous chondrocyte implantation is a technique for repairing articular cartilage defects in the knee. Despite reported improvements in pain, little is known about the recovery of knee biomechanics during walking gait. Methods A randomized controlled study design was used to investigate knee biomechanics during gait in 61 patients following matrix-induced autologous chondrocyte implantation, in conjunction with either 'accelerated' or 'traditional' approaches to post-operative weight-bearing rehabilitation. Gait analysis was performed at 3, 6 and 12 months post-surgery in both patient groups, and two matched, unaffected control groups for comparison. Findings The spatiotemporal and ground reaction force parameters were similar between patient groups and their respective control groups at all time points. When compared with controls, both patient groups demonstrated significantly reduced knee extension moments up until, and including, 12 months. The traditional group demonstrated a significantly reduced knee adduction moment at 3, 6 and 12 months, and a significantly reduced knee flexion moment at 3 months. There were no differences in these knee moments between the accelerated patient group and controls. Interpretation Overall, a higher level of gait dysfunction was observed in patients who underwent traditional rehabilitation. Future research is needed to investigate the recovery of normal gait following matrix-induced autologous chondrocyte implantation, and its effect on repair tissue development.