Background <p>Insufficient quadriceps activation is likely to occur in the early postoperative period after anterior cruciate ligament reconstruction (ACLR). Transcranial magnetic stimulation (TMS) has a positive effect on the activation and contractility of the quadriceps femoris. To investigate the effect of repetitive transcranial magnetic stimulation (rTMS) on quadriceps femoris function in participants during the early postoperative period following anterior cruciate ligament reconstruction (ACLR).</p> Methods <p>Fifty six participants received rehabilitation education and a recommended routine training and knee flexion and extension exercise plan. In addition to this, the REAL group received 2 weeks of transcranial magnetic stimulation treatment. The resting motor threshold (RMT), root mean square (RMS) value, difference in knee extension angle between the healthy and affected sides, visual analog scale (VAS) score, and difference in the circumference of the vastus medialis oblique between the healthy and affected sides were assessed at baseline and 2 weeks after treatment.</p> Results <p>Compared with those in the SHAM group, the improvements in the RMT and RMS value of the vastus medialis oblique, the difference in the knee extension angle between the healthy and affected sides, and the VAS score in the REAL group were more significant (<i>p</i> &lt; 0.001). There was no significant between-group difference in the difference in the circumference of the vastus medialis oblique between the healthy and affected sides (<i>p</i> &gt; 0.05).</p> Conclusion <p>The use of rTMS, the goal of which is to increase the excitability of the corticospinal pathway, can promote the activation of the quadriceps femoris, prevent muscle atrophy, and accelerate the recovery of muscle strength in participants in the early postoperative period after ACLR.</p> Trial registration <p>The Registration number of the Chinese Clinical Trial Registry is ChiCTR2300076522, 11/10/2023.</p>